FEI Helios NanoLab 600 SEM/FIB Basic Operation Procedure
Emergency contact: Dr. Kai Song, 1-6467 (O), 860-786-8121 (cell), songka@mst.edu
Special Notes or Restrictions:

Do not attempt to start the instrument if either the red OFF button light or the yellow STANDBY button light
on the front panel is illuminated (see the picture below), contact AMCL staff.

Always view the chamber camera when moving the specimen stage.

When screwing sample holders onto the stage or sample onto the sample holder, do not over tighten.

Never insert retractable STEM detector or EBSD detector when standard Universal Mount Base (UMB) is in the
chamber.

Never use force to open the chamber. Wait until chamber is fully vented.

Always make sure that the chamber has been pumped down to high vacuum before leaving the room.
Sample Preparation
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
Always wear gloves when handling SEM/FIB components!

Secure sample to stub with spring, carbon tape, adhesive tabs and/or carbon paint.

Dry/heat carbon paint to remove solvent before putting into chamber.

Sample should be less than 10mm tall. If larger please see AMCL staff.
Section 1 – System Starting and Sample Loading
1. Verify Vacuum status – all three chambers in the diagram at the bottom-right should be green (Fig. 1).
2. Open gas cylinder (main valve) and vent the chamber with Vent button (Fig. 2). Note: never use force to open the
chamber. Wait until chamber is fully vented (6-8 min).
3. Mount the sample onto the appropriate holder. Please check the separate manual pages on sample mounting for
reference.
4. When the chamber is vented, gently pull out the chamber door and stage. Never force the door open or press on
the chamber door. Turn off the gas cylinder.
5. Mount the holder/sample onto the stage. Please note that your sample should be <8mm tall, for EDX, less than
5mm tall. If you are loading multiple samples, they must all be within 1mm of the same height.
6. Gently close the chamber door and press the Pump button (Fig. 2). When moving the stage, view the chamber
camera image when the sample is in close proximity to SEM pole piece. Keep holding the door until the noise
from scroll pump becomes quiet. Wait for the chamber vacuum status to turn green (~6min).
7. If you are just using E beam, select the E beam quadrant (left clicking the top left quadrant – default for E beam)
and click Beam On (Fig. 2). The icon will turn yellow.
8. If you are using both E beam and I beam (i.e. FIB work), click Wake Up button to start both E and I column
(Fig. 2). If the system has already been woken up, simply click Beam On for both E beam and I beam.
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Section 2 – Setting Up Electron Column
1. Select the top-left quadrant (default quadrant for E column; top-right is for ion column).
2. Zero Beam Shift for E column. (Fig. 3).
3. Select the desired High Voltage and Beam Current for the E column. 5kV and 43pA is recommended for start.
4. Check that the ETD detector is selected (Fig. 3). Turn on E beam by clicking Beam On (if not done yet).
5. Locate the sample and focus on the sample surface. You can navigate by moving the mouse while holding down
the middle mouse button (scroll wheel). A yellow circle with arrow should appear on screen when you are moving
the sample (Fig. 4c, next page). Correct X/Y stigmation. Click “F2” key to take an image.
6. Click “link Z to FWD” (Fig. 3). Read the Z value from Navigation tab. This step is to find the correct working
distance, which is an important parameter for SEM. Note: You will have to click on this button each time you
change the focal distance because the system links the Z axis to the focal distance and not the reverse.
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Section 3 – Alignment of Electron Column
1. Make sure all conditions are set (high voltage, beam current, working distance, etc.).
2. Select the E beam quadrant.
3. Focus on a small particle on the sample surface with magnification >10,000X.
4. Adjust the Stigmator (using front panel or the Beam Control Tab) to achieve the sharpest image and to minimize
stretching during focusing.
5. (Optional) Turn on Crossover (Fig. 4a). Adjust the Source Tilt (dragging the small rectangle using mouse) to bring the
circle to screen center (Fig. 4b). Turn Crossover off.
6. (Optional) Turn on Lens Align (Fig. 4a). Adjust the Lens Alignment (dragging the small rectangle using mouse) to
minimize translation of the image. Turn Lens Align off.
7. Focus and adjust stigmator again on the small particle. Note: a reduced window
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helps fine tuning (Fig. 3).
Section 4 – High Resolution E Beam Imaging
1. Set desired high voltage and current. 5kV and 43pA is recommended for high resolution imaging in Immersion mode.
2. In Field-free mode (default mode), go to area of interest, focus sample and correct stigmation.
3. Make sure the sample is in focus. Link Z to FWD (Fig. 3). Read the “Z” value in the Navigation tab (Fig. 6). Lower Z
to around 4-5 mm. Focus sample again.
4. Choose Immersion Mode (Fig. 5). There are two modes available on the Helios:
a) Mode 1 – Field-free mode, useful for low magnification imaging, imaging during ion milling and magnetic sample.
b) Mode 2 – Immersion mode, useful for high resolution/high magnification imaging (sample immersed in lens field,
better focusing of e beam, a powerful magnetic field between SEM-column and sample). For the immersion mode, the
minimum magnification is about 1000x and the working distance usually is around or less than 5mm. A minimum
working distance should be larger than 2 mm.
5. Focus specimen and correct stigmation in Immersion mode.
6. Align Source Tilt and Lens Alignment in Immersion mode as described in Section 3. Note: alignment is separate for
the Field-free and Immersion modes. Re-alignment is necessary when switching modes.
7. Fine Focus, correct stigmation and take high resolution images.
8. When you finish high resolution imaging, return to Field-free mode. Focus and correct stigmation again. Re-align
Source Tilt and Lens Alignment in Field-free Mode.
Note:- never load ferromagnetic particles in immersion mode! The strong field can attract magnetic particles into the pole
piece. If a bulk magnetic sample is to be examined in immersion mode, make sure the sample has been firmly fastened to
the stub so that it won’t bump onto the pole piece by the field!
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Section 5 – Setting Up Eucentric Height (FIB work)
1. Send the stage to a 5 mm working distance (Z=5) under the Navigation tab.
2. Focus and relink Z to FWD.
3. Align a feature on the sample to the center cross on the screen. Set mag  3500. Tip: double-click a feature to move it
to screen center.
4. Tilt the column at 5° and check if the feature has moved on screen (Fig. 6a, b).
5. Make sure that the lower right CCD quadrant is selected (left click it using mouse). Adjust the Z-axis of the stage to
bring the feature back to center by holding medium mouse button and dragging the yellow bar (arrowed in Fig. 6c) up or
down.
6. Tilt back to 0° and repeat the above steps until you have minimized longitudinal shift of the feature when tilting (Fig.
6d). Small lateral movement during tilting is OK.
7. Repeat the steps 3  6 at 15° tilt. The final eucentric height should be around 4.10.1 mm.
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Section 6 – Setting Up the Ion Column and Beam Coincidence (FIB work)
1. To turn on the ion beam, select the appropriate quadrant (top-right) and select Beam On under the beam control tab.
2. Zero the beam shift for both electron and ion column (Fig. 3).
3. Set Scan Rotation to zero for both E and I column (Fig. 7).
4. Check the “Couple Magnification” box (Fig. 2). This is to maintain the same magnification between E and I column.
5. Set the desired High Voltage (usually 30kV) and Beam Current for the ion column.
 For ion imaging, choose low currents (<48pa) to minimize sample damage. Keep in mind that ion imaging
simultaneously causes surface damage and Ga implantation.
 For ion milling, higher currents will allow for better throughput, but result in a larger beam.
6. Make sure eucentric height has already been done. Align a feature in the electron image with the center cross.
7. Tilt the stage to 52° in the navigation tab. Re-align the feature to the center cross in the electron image (double-click
the feature on screen).
Note: If there is a significant shift of the feature position, the eucentric height has not been set up correctly. Tilt back
to 0° and repeat the steps under Setting Up Eucentric Height (Section 3).
8. Switch to the ion column image and adjust the Image Shift (knobs on front panel) to re-align the same feature to the
center cross – the electron and ion beams are now coincident.
Note:- You can use either the front panel or the Beam Control Tab to adjust Magnification, Beam Shift, Stigmator,
Brightness and Contrast, etc.
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Section 7 – Ion Beam Imaging (FIB work)
Ion beam imaging is used for FIB processes such as milling, Pt deposition, cleaning, etc. Ion beam also provides an
additional contrast for imaging, i.e. ion channeling contrast.
1. Select ion column quadrant (top right). Set desired ion beam parameters. Unlike E beam imaging, the ion beam imaging
is a destructive process during which the surface of the sample is continuously sputtered by the ion beam. Thus one should
use a small ion beam current for imaging purpose. 9.7pA or 27Pa is recommended. 30kV is default for ion imaging.
2. Adjust Focus and Stigmator to achieve the sharpest image and minimize stretching during focusing. To prevent the
viewed area from being sputtered during focusing, one may correct focus and stigmation in an adjacent region and shift
back to the area of interest upon finish.
3. An example of E beam imaging and I beam imaging for the same area is shown in Fig. 8: a) E beam image; b) I beam
image. The contrast in b) is ion channeling contrast, which highlight grain structure of polycrystalline material.
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Section 8 – General Patterning Instructions (FIB work)
1. There are simple patterning tools accessible under the patterning tab (Fig. 7). Rectangle, Cleaning Cross Section and
Regular Cross Section are the most frequently used.
2. A different operation (ion/electron exposure, deposition, etc.) and set of parameters (dimension, current, voltage, dwell
times, etc.) can be assigned to each shape.
3. You may set up a sequence of different shapes and operations.
4. More complex geometry and exposure control can be achieved by importing bitmaps (raster scan, the brighter, the
longer the dwelling time) or generating scripts (arbitrary pattern).
5. Common milling/Pt deposition parameters:

Regular cross-section – Si, 9.3nA; Cleaning cross-section – Si, 0.28-2.8nA; Pt deposition – Pt, 48pA – 0.28nA.

30kV is default for all operation.
Note: focus and stigmation need to be adjusted each time when the ion beam current is changed.
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Section 9 - Pt Deposition (FIB work)
1. Only Pt deposition is currently available on the Helios.
2. Turn on crucible heating (Fig. 10). The crucible should be warmed for a minimum of 15 minutes prior to deposition to
achieve uniform deposition.
3. Deposition can be carried out with either the electron or ion beam. Ion beam deposition is common for most
applications. 93pA or 0.28nA at 30kV are recommended.
Note: Electron beam induced deposition may be chosen when sputtering of the sample surface needs to be avoided.
The E-beam deposition must be conducted at 0 degree tilt. Please see Dr. Kai Song for more information.
4. Make sure the sample surface is already at eucentric height. The Pt deposition needle is only ~ 100 m above
eucentric height. The GIS needle may hit the sample surface if the sample is above eucentric position!
5. Insert the GIS (Gas Injection System) needle by clicking the check box under the patterning tab (Fig. 10). Refer to the
General Patterning Instructions to use the GIS (this will open and close the gas valve automatically). Otherwise, once
the gas valve is open and the beam is on, deposition/etching will occur in the area being viewed.
6. Retract the GIS needle (uncheck the box in Fig. 10).
7. When you are completely done with a GIS, turn off the crucible heating.
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Section 10 - Shut Down and Sample Removal
1. Remove GIS, Omni probe, STEM detector or EBSD detector if you have used any of these. Turn off GIS heating.
2. Switch back to field free mode if you have used immersion mode. Switch back to ETD detector if you are using other
detectors.
3. Set X=Y=Rotation=Tilt=0 in the Coordinate tab (the
tab). Leave Z as is.
4. Open gas cylinder and click “Vent”.
5. Wear gloves. Wait (about 6 minutes) until the specimen chamber is fully vented. Gently pull out the chamber door.
6. Remove the specimen and whatever holders you have used (i.e. stub module, clamp bars, row holder, STEM holder
and EBSD holder). If you are using the Universal Mount Base, leave it in the chamber.
7. Close the gas cylinder.
8. Gently push and close the specimen chamber door and click “Pump”
9. Hold the chamber door for at least 30 sec with a moderate pressure to keep it tight. The pump noise will become quiet.
It is recommended that the user continues holding the door until the chamber pressure reading changes from
“unknown” to a value (about 4 minutes).
10. Remove sample and put holders, stub module and clamp bars back into the clear plastic cover.
11. Fill in the log book. If you are the last user of the day, put system to “Sleep”.
12. Check and make sure the chamber vacuum has returned to high vacuum (color becomes green) before leaving the
room.
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