Using the Multi-Mode Scanning Probe Microscope (MM SPM)
TappingMode
This manual describes the steps of everyday use of the SPM, specifically in its capacity
as an Atomic Force Microscope (AFM) in TappingMode. Little to no experience is
required. There are basically six tasks or activities that you will perform while using the
microscope, and they are:
0.
1.
2.
3.
4.
5.
6.
Learning Equipment Terminology…………
Setting up for Microscope Usage………….
Taking an Image…………………………………
Viewing Your Image……………………………
Modifying Your Image………………………….
Analyzing Your Image…………………………
Shutting Down……………………………………
Pg
Pg
Pg
Pg
Pg
Pg
Pg
2
3
7
11
13
14
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You may want to shut down the equipment without viewing, modifying, or analyzing
your image(s), in which case you may simply skip sections 3, 4, and/or 5.
Some subsection titles are followed by notes referring to sections of the Multimode
Scanning Probe Microscope Instruction manual (SPMI) and the Command Reference
Manual (CRM) for further reading.
To the microscope!
1
0. Learning Equipment Terminology
Here are diagrams of the microscope for your reference (from SPMI Ch. 2; 2.1)
Figure 0.1 The Multimode SPM
Major components:
1. laser
2. mirror
3. cantilever
4. tilt mirror
5. photodetector, or
photodiode array
Figure 0.2 The SPM head and major components
2
1. Setting up for Microscope Usage
1.1 Turn on the Equipment
 First turn on the computer and the two monitors. (The on/off switches have
circles with vertical lines in them.)
 When the “Begin Logon” window appears, press the “Ctrl”, “Alt”, and
“Delete” keys (in that order, releasing them at the same time) to log on.
 Start up Windows by clicking on the “OK” button on the “Logon
Information” window that appears next. (There is no need to enter a
password.)
 Double-click on the “Nanoscope v4.43r8” icon to enter the program that
controls the microscope and displays the images. Wait for two windows to
open, one on each monitor.
 Turn on the Nanoscope III Scanning Probe Microscope Controller by pressing
the switch located on the back side of the Controller in the top corner farthest
away from the monitors. (If you plan on viewing/modifying/analyzing images
without actually using the microscope, you do not need to turn on the
Controller.)
1.2 Place the Sample in the Microscope
 Slowly take the metal cover off of the microscope.
 Release the clamp that secures the tipholder by turning counterclockwise the
knob in the center of the back side of the head.
Note: Turning directions are given as if the user were viewing the screw along
the axis of the screw from the side of the knob.
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
Carefully remove the tipholder from the head, holding the tipholder by the
finger-grip rod (watch out: the finger-grip is a little loose!), and place it upside
down in a safe place where nothing will damage the exposed tip.
You should ask someone to make sure the correct tip is in the tipholder for
TappingMode. You should also learn how to change the tip. (It is probably
best to learn how to change the tip by watching and doing rather than by
reading.)
Use the puck tweezers to pick up the puck that holds the sample of interest.
When moving the sample, keep your hand just below the puck so it does not
accidentally fall.
Place the puck onto the circular stage inside the head. The stage is magnetic
so the sample is held stably.
3

(Read the warning before performing this step.) Return the tipholder to the
head, being cautious not to damage the sample when moving the tipholder
above the sample.
Warning: When the tipholder is positioned over the sample, the tip must not
touch the sample or it may break the cantilever. If it looks like they might
touch when you are lowering the tipholder into place, take the tipholder out
and do not put it in the head until the contact balls have been raised. (See 1.3)

Once the tipholder is placed in the head above the sample, secure the tipholder
by turning clockwise the knob in the center of the back side of the head until
the tipholder is clamped in place.
1.3 Adjust the Microscope (see SPMI Ch. 8; 8.3.2)
 The Probe – The probe moves as a unit with the head, which sits on the X-Y
head translator and three contact balls. The translator controls the horizontal
positioning of the probe, and the elevation of the contact balls determines the
vertical positioning and tilt of the probe.
o While watching the probe with the Specwell microscope, lower the
probe using the coarse adjustment knobs below the scanner support
ring. Turn each knob counterclockwise to lower its respective contact
ball. (The motor control switch controls the elevation of the third
contact ball.)
o The probe should be as close to the sample as possible without
touching it so that the probe does not have far to travel when the
microscope engages the tip with the sample surface. The cantilever is
100 micrometers long, and the tip should be less than 130 micrometers
from the sample surface, so length of the cantilever can be used to
judge if the probe is positioned close enough.
o If you want to position the probe above some specific feature on the
sample, watch the probe with the Specwell microscope through the
window at the top of the head while you turn the knobs of the X-Y
head translator.
Warning: The probe must not be too low when you move it
horizontally or else the cantilever may break when dragged across a
tall feature of the sample.

You may want to illuminate the sample with the Fiber-Lite when
viewing it through the top window.
The Laser Beam – The laser beam must be centered at the end of the
cantilever to be reflected back to the tilt mirror and to the photodiode array, or
photodetector. An easy way to position the beam correctly is to use the paper
method…
o The Paper Method: Place a small piece of paper between the tipholder
and the left inside wall of the head. Turn the tilt mirror by pressing
down on the mirror lever so that the laser beam is reflected onto the
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
piece of paper. Watch the probe with the Specwell microscope while
turning the laser adjustment knob at the front of the head
counterclockwise; you will see the laser beam travel to the left along
the cantilever. Watch the paper as the reflected beam becomes less
focused and then disappears as the beam travels beyond the tip of the
cantilever. Turn the knob clockwise until the red dot reappears and
becomes focused. Then turn the other laser adjustment knob back and
forth to find the most focused position for the beam across the
cantilever.
o If you would like to use another method or are having trouble getting
the beam positioned on the cantilever in the first place, try this: Look
through the window at the top of the head with the Specwell
microscope, watching the probe and the laser spot as you position the
laser beam at the end of the cantilever with the laser adjustment knobs.
Note that there is some parallax in the position of the laser spot with
respect to the cantilever.
The Mirror – As much as possible of the laser light reflected from the tilt
mirror must reach the photodetector. Adjust the position of the tilt mirror
lever so that the signal sum display reads a maximum signal. For
TappingMode, the maximum signal is a little under the 3.6 V level.
The Photodetector – The laser light must be centered on the photodetector, so
the horizontal and vertical position of the photodetector must be adjusted.
o Horizontal centering: Flip the mode selector switch to the “AFM &
LFM” setting so the lower numerical display gives a reading of the
horizontal difference, or the horizontal deflection of the beam from the
center of the photodetector. (The light above the displays on the base
will become red.) Use the photodiode adjustment knob located on the
back side of the head to get a reading close to zero volts. A value
between –0.15 V and 0.15 V is adequate. Turn the knob clockwise to
increase the reading. (It may take a few turns for the number to
change when it starts from an extreme value.)
o Vertical centering: Flip the mode selector switch to the “TM AFM”
setting so the lower numerical display gives a reading of the vertical
difference, or the vertical deflection of the beam from the center of the
photodetector. (The light above the displays on the base will become
green.) Use the photodiode adjustment knob located on the top of the
head to get a reading close to zero volts. A value between –1.00 V and
1.00 V is adequate. (The reading can waver by almost 1.00 V, so the
value should be set somewhere near zero, then watched to be sure that
it doesn’t go beyond –0.50 V or 0.50 V.) Turn the knob clockwise to
increase the reading. (It may take a few turns for the number to
change when it starts at an extreme value.)
o If the difference readings jump around uncontrollably, the probe may
be touching the surface of the sample, so you must raise the tip and
adjust the photodetector position (and possibly the mirror) again.
5
o Remember that after the position of the photodetector has been
adjusted, the mode selector switch must be on the “TM AFM” setting
for taking images in TappingMode.
1.4 Tune the Cantilever (see SPMI Ch. 8; 8.3.4)
 On the left control monitor, click on the microscope icon in the top left corner
of the “Nanoscope Control” window. This button accesses the real-time
operation and control of the microscope while the other button accesses the
off-line program operations such as viewing, modification, and analysis of
images.
 Look at the bottom of the “Nanoscope Control” window and make sure that
“Tapping AFM” is written to the right of “Extended Multimode.” If it isn’t
written (perhaps “Contact AFM” is there instead), then click on “Microscope”
at the top of the “Nanoscope Control” window and select “Profile.” Select
“!Tapping AFM” and click on “Load.”
 Look in the “Other Controls” sub-window to make sure that the “Microscope
mode” is set to Tapping.
 Click on the blue tuning fork icon (the third icon from the right) at the top of
the window to access the cantilever tuning controls.
 In the “Cantilever Tune” sub-window set the following parameters to their
associated values, if they are not set already:
o Start frequency: 50 kHz
o End frequency: 500 kHz
o Target amplitude: 3 V
o Peak offset: 5 %
 Click on the “Auto Tune” button in the “Auto Tune Controls” sub-window.
 Wait for the “Auto Tune” sub-window to disappear when auto tuning is
complete.
 The sweep should look something like this (drive frequency ~300 kHz):
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
Click on the eye icon in the top right corner of the “Nanoscope Control”
window to return to the real-time control sub-windows.
The Drive frequency in the “Feedback Controls” sub-window is now set to its
appropriate value, and the Amplitude setpoint and Drive amplitude are set to
appropriate initial values.
6
2. Taking an Image
2.1 Enter the Initial Settings (see SPMI Ch. 8; 8.3.1 and 8.3.3)
 For each category, enter the appropriate initial settings:
 “Scan Controls” sub-window
o Scan size: You can enter a scan size from the nanometer level to about
150 micrometers, but you’ll probably want to start with a value of at
least 1 micrometer.
o Aspect ratio: An aspect ratio of 1:1 will produce a square image, and
the other ratios produce different sizes of rectangle. Click, hold, and
drag the mouse button on the ratio to select the desired values.
o X offset: Start with a value of 0.
o Y offset: Start with a value of 0.
o Scan angle: Start with a value of 0.
o Scan rate: Start with a value of 1 Hertz.
o Tip velocity: When you specify scan rate, tip velocity is already
configured.
o Samples/line: Start with a value of 512.
o Lines: Start with a value of 128.
o Slow scan axis: Start with the slow scan axis enabled.
 “Feedback Controls” sub-window
o Integral gain: Start with a value of 0.3000.
o Proportional gain: Start with a value of 0.3000.
o The Amplitude setpoint, Drive frequency and Drive amplitude values
have already been set in the auto tuning process.
 “Other Controls” sub-window
o Microscope mode: The mode should be set on “Tapping.”
o Z limit: The value should be at its maximum (for bumpy samples).
o Units: “Metric” should be selected.
o Color table: The color table determines the color scheme of the image.
Possible values range from 0 to 21. I suggest using 2, 4, 5, or 12.
o Engage setpoint: The value should be 1.00.
o Min. engage gain: The value should be 3.00.
 “Channel 1” sub-window
o Data type: “Height” should be selected.
o Data scale: Start with a value of 6.292 um.
o Line direction: “Trace” should be selected.
o Scan line: “Main” should be selected.
o Realtime planefit: “Line” should be selected.
o Offline planefit: “None” should be selected.
 “Channel 2” sub-window
o This should be the same as the “Channel 1” sub-window, except
“Retrace” should be selected for the Line direction.
 “Interleave Controls” sub-window
o Interleave mode: “Disabled” should be selected.
7
2.2 Engage (see SPMI Ch. 8; 8.4)
 Look at the base of the microscope and check that the light is green and the
lower numerical display reads a vertical difference between –1.00 V and 1.00
V.
 Click on the engage icon, which has a picture of a cantilever and a green
arrow pointing downward. (The disengage button has the red arrow pointing
upward.) If an “Engage” sub-window appears that asks, “Interleave mode is
enabled – continue?” then click on “No” and set “Interleave mode” to
“Disabled” in the “Interleave Controls” sub-window and click on the engage
icon again (re-engage).
 An “Engage Status” sub-window appears and the tip lowers to engage with
the sample surface. Once the tip is engaged, the computer will beep, the
“Engage Status” sub-window will disappear, and an image will start to appear,
line by line, in the “Nanoscope Image” window on the right display monitor.
 If the engaging process takes a long time and the “Motor” reading at the
bottom of the “Nanoscope Control” window surpasses about 130 micrometers,
you should abort the engaging process and trouble-shoot. Perhaps you did not
position the probe close enough to the sample, or perhaps the head is tilted too
much, causing the back contact ball to lose contact with the head as it is being
lowered.
2.3 Adjust the Settings (see SPMI Ch. 8; 8.6)
 Click on the icon with the picture of the oscilloscope image (next to the eye
icon) to bring up the real-time trace and retrace image on the display monitor.
The two lines should match very closely after adjustments have been made.
 Decrease the Amplitude setpoint (a.k.a. setpoint) until the trace and retrace
lines begin to show some distinct features, indicating that the tip has indeed
made tapping contact with the surface.
 The Z-level indicator on the right side of the “Nanoscope Image” window
may bounce up and down a little, or it may remain high for a few seconds
while you decrease the setpoint, but as you continue to decrease the setpoint,
the Z-level should become more stable and begin to lower.
o If the bar is high and the red “Z-limit” warning appears, the vertical
piezoelectric element is retracted and the tip is probably not in contact
with the sample. If the bar is low and the red “Z-limit” warning
appears, the element is extended and the tip may or may not be in
contact with the sample.
o If at any point in scanning the red “Z-limit” warning appears and you
can’t adjust the setpoint to get rid of the Z-limit warning and keep a
decent scan trace and retrace, you should disengage and reengage so
that the probe is repositioned at a more moderate distance from the
vertical piezoelectric element.
 When the tip encounters some bumpier features set the Slow scan axis to
“Disabled” so the probe scans the same features over and over again. That
8
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way, you will be able to see how your adjustments improve an individual
scan.
If the scans are very flat or the scans do not vertically cover much of the
oscilloscope screen, decrease the Data scale for Channels 1 and 2 until the
scan takes up about two-thirds of the oscilloscope screen.
Some adjustments that should be made are bulleted in the approximate order
of importance:
o Amplitude setpoint: Further decreasing of the setpoint may help the
scan lines to match up. (The Z-level reading will probably end up in
the lower third of the bar.)
o Integral gain: Increasing the integral gain will cause the lines to match
more closely, effectively increasing the sensitivity of the feedback
loop. Increase the gain until you start to see noise in the signal, and
then decrease it a little to rid the signal of the noise.
o Proportional gain: It can usually be set a factor of 5-10 times larger
than integral gain. (Most manuals suggest increasing the proportional
gain until noise appears, and then decreasing it to get rid of the noise,
but we usually find it unnecessary to keep increasing it beyond the 10
times larger than the integral gain.)
o Scan rate: Decreasing the scan rate will help to match the trace and
retrace lines, especially if the sample is particularly bumpy or rough.
o Drive amplitude: If the sample is dirty or sticky, it may be impossible
to get a streak-less image with the given initial setting for the drive
amplitude.
Warning: Excessive increase of the drive amplitude can fracture the
cantilever. Increase the drive amplitude incrementally.
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To increase the drive amplitude, first increase the amplitude setpoint
until the Z-level reaches the fully retracted position, note the voltage at
this level and continue increasing the setpoint to a level 2 volts above
the noted value. Then increase the drive amplitude by pressing the
right arrow key 2-3 times. Finally, reduce the amplitude setpoint back
down to resume scanning the sample. (You will not have to reduce the
setpoint as much as you increased it.)
When the trace and retrace match adequately, set the “Slow scan axis” to
“Enabled” so the probe scans the entire area specified in the “Scan size”.
Click on the eye icon to see how the image is turning out and to see if the area
is good enough to be scanned. (If there are large, unwanted features, you may
want to disengage, reposition the probe or sample, and reengage.)
Once the entire scan area has been scanned, increase the “Lines” in the scan to
256 or 512, depending on the resolution you want.
Make any further adjustments that are necessary to make scan lines consistent
with each other and produce a good image. (If no adjustments seem to help
correct problems, you may want to consult the troubleshooting sections of the
SPMI: Ch. 15, 15.10.15 through 15.10.19)
9
2.4 Capture an Image (see CRM Ch. 5)
 Capturing an image means to save the scanned image as a file for viewing,
analyzing and modifying.
 To capture an image, you must first name the prospective image file. Click on
“Capture” at the top of the “Nanoscope Control” window while the
microscope is still scanning the sample and select “Capture Filename.”
 Type a name for the image file you will create. The convention we are using
is to start with the name of the person using the microscope, then write the
date and a period, and end with the ordinal number of the image for that day.
For example, a filename could be Sue1031.001.
 When you think you are getting a good scan and want to capture the image,
click on “Capture” and select “Capture.” If no adjustments have been made
since the probe started a new sweep of the scan area, the status notification
“Capture On” will appear at the bottom of the “Nanoscope Control” window
and capturing will be completed when the probe has finished scanning the
area. If adjustments have been made, the status notification “Next” will
appear, and capturing will start on the next sweep of the scan area. If you
select “Capture” again, the capture process will be “Forced” to occur on the
present sweep.
 After you capture the first image, the following captured images will be
named automatically, with the ordinal number increasing by one with each
additional image. (Sue1031.002, and so forth.)
 It is good procedure to take at least two images of the same area so they can
be compared to reveal artifacts and glitches.
2.5 Disengage
 When you are done capturing images, just click on the disengage icon, which
has a picture of a cantilever and a red arrow pointing upward.
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3. Viewing Your Image
3.1 Select an Image (see CRM Ch. 8)
 First, click on the colorful icon in the upper right corner of the “Nanoscope
Control” window to access the off-line program operations such as viewing,
modification, and analysis of images.
 A “Files” sub-window appears with drives listed at the top. Initially, the “!”
drive is selected and the images you have captured are listed on the right
section of the “Files” sub-window, probably along with other previously
captured images.
 Select the specific file you want to view by double-clicking on its name. A
top-view image will immediately appear in the “Nanoscope Image” window.
(Do not worry if your image looks nothing like it did when you scanned it;
you will have to follow steps in Section 4, “Modifying Your Image,” to
correct the image. In the meantime, you can look at other images. More
images can be found in the “d” drive in /images, /v443r8/capture, and
/v443r8/tutorial.) You can also use the arrow keys and the “Enter” key to
select images.
3.2 Select a Viewing Option (see CRM Chs. 9, 10)
 If the image is composed of two images, click on “Image” at the top of the
“Nanoscope Control” window and select either “Select Left Image” or “Select
Right Image.”
 Then click on “View” and select from one of the following viewing options:
o “Top View.” This view is the same as the initial view that appears when
scanning an image and when you select an image.
o “Line Plot.” This view is a “three-dimensional” image made thin lines
that follow the trace pattern of the probe. This view makes it easy to see
the behavior of each individual trace while at the same time giving you a
perspective of the whole image.
o “Surface Plot.” This is a “three-dimensional” image where the trace lines
are connected to reveal a surface.
o “Quick Surface Plot.” This view is similar to the Surface Plot image,
except the image is smoother, with less resolution, and fewer parameters
are displayed.
 Each view brings up its own sub-window on the control monitor, allowing
you to change aspects of the view to make different features more or less
visible.
 To change from one view to another, or to access other program functions
dealing with image modification and analysis, you must first click on the
“Quit” button of the viewing sub-window.
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3.3 Experiment with the Viewing Parameters (see CRM Chs. 9,
10)
 Each viewing sub-window has a set of parameters that affect the presentation
of the data of the image. (These parameters do not alter the data of the image,
although the “Data scale” can cut off high and low points if it is too low.)
 The parameters can be changed with the keyboard (arrow keys and sometimes
number keys) and the mouse (click, hold, and drag).
 Try every view and experiment with different values for each parameter.
3.4 Add or Edit a Note
 It is a good idea to add a note to each image to describe the sample and
perhaps which mode was used when it was imaged.
 When in one of the viewing sub-windows, click on the “Note” button, type a
note, and then click on the “Ok” button. You can then click on the “Quit”
button.
 When you select another image, a “Save” sub-window will appear asking if
you want to save the image you modified with a note: click on “Yes,” and
then on “Ok” in the “Save As” sub-window.
3.5 Create Your Own Directory
 You should create a directory in which to keep all of the images you scan.
Click on “File” and select “Create Directory.”
 Type “d:\v443r8\” followed by your name into the field in the “Create
Directory” sub-window (e.g. d:\v443r8\Sue).
 Select the “!” drive to access the images you have recently taken.
 Select one of your files, and then highlight all of the files of images you have
taken. (If all of your files are lined up in a row, you can click on the top one,
press and hold the “Shift” key, click on the bottom one, release “Shift”, and
your files will be highlighted. If your files are separated, you can click on
each one individually while pressing the “Ctrl” key to highlight each one.)
 Click on “File” and select “Move”. In the “Move” sub-window, type the
location of your directory (e.g. d:\v443r8\Sue), click on “Ok”, and click on
“Ok” in the “Move Confirm” sub-window.
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4. Modifying Your Image
4.1 Copy Your Image (see CRM Ch. 8; 8.8)
 If you have not already done so, click on the colorful icon in the upper right
corner of the “Nanoscope Control” window to access the off-line program
operations such as viewing, modification, and analysis of images.
 Select the image you captured, click on “File,” and select “Copy.”
 Enter the name of the new image: click to the right of the highlighted text, reenter the date of the image, a period, the number of the image (with one less
zero on the right), and the letter “a.” Additional modified versions of the
image can end with the following letters of the alphabet.
4.2 Correct Your Image (see CRM Ch. 13; 13.6)
 Select the new, copied image, click on “Image,” and select either “Select Left
Image” or “Select Right Image.”
 Click on “Modify” and select “Flatten.”
 Read the “Warning” sub-window and click on it to make it disappear.
 Make sure that the “Order” is 1.
 Click on “Execute.”
 Click on “Save” or “Quit.” Choosing “Quit” will allow you to keep
modifying the image without saving the changes, or to save the changes at
another point.
4.3 Experiment with the Modification Options (see CRM Ch.
13)
 Try all of the modification options, undoing each of them, or quiting each
modification operation and reselecting the image to modify it again.
 Each type modification works best to improve particular kinds of images, of
course, so try modifying some of the other images too. (Don’t save the
changes unless you mean too, and keep the original image untouched.) For
example, the “Lowpass” filter modification works best with an image with
high frequency noise.
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5. Analyzing Your Image
5.1 Take a Cross-Section (see CRM Ch. 12; 12.6)
 If you have not already done so, click on the colorful icon in the upper right
corner of the “Nanoscope Control” window to access the off-line program
operations such as viewing, modification, and analysis of images.
 Select an image, click on “Analyze,” and select “Section.”
 At the bottom of the “Nanoscope Image” window there is a top view of the
image you selected. You can draw lines by clicking on the image to
determine the angle of a cross-section graph of the surface of the sample.
 Two arrows on the cross-section graph, which are movable by clicking on
them, allow you to obtain information about features of the surface, visible in
the table on the right.
5.2 Read about the Analyze Options (see CRM Chs. 12, 13)
 You can experiment with each of the analyze options, but it may be better to
read about them first.
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6. Shutting Down
6.1 Put the Sample Away
 Release the clamp that secures the tipholder by turning counterclockwise the
knob in the center of the back side of the head.
 Carefully remove the tipholder from the head, being cautious not to damage
the sample when moving the tipholder above the sample, and place it upside
down in a safe place where nothing will damage the exposed tip.
 Use the puck tweezers to move the sample to its container. Remember when
moving the sample to keep your hand just below the puck so it does not
accidentally fall.
 Return the tipholder to the head and secure the tipholder.
 Slowly place the metal cover back on the microscope.
 Put the covers back on the Specwell microscope, and put away any other tools
used.
 Keep your samples in a secure place, such as a covered petri dish in the desk
or in the Dry Keeper case.
6.2 Turn off the Equipment
 Turn off the Nanoscope III Scanning Probe Microscope Controller.
 Click on the small x in the top right corner of one of the main windows.
 Shut down windows. (Click on the “Start” button, select “Shut down,” and
click on “Yes.”)
 Turn off the computer and the two monitors.
 Clean up after yourself.
15