August 2012 

NASA/TM–2012-217597 

Transmission Electron Microscopy (TEM) 

Sample Preparation of Si1–xGex in c-Plane 

Sapphire Substrate 

Hyun Jung Kim 

National Institute of Aerospace, Hampton, Virginia 

Sang H. Choi 

Langley Research Center, Hampton, Virginia 

Hyung-Bin Bae and Tae Woo Lee 

Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea 
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August 2012 

NASA/TM–2012-217597 

Transmission Electron Microscopy (TEM) 

Sample Preparation of Si1–xGex in c-Plane 

Sapphire Substrate 

Hyun Jung Kim 

National Institute of Aerospace, Hampton, Virginia 

Sang H. Choi 

Langley Research Center, Hampton, Virginia 

Hyung-Bin Bae and Tae Woo Lee 

Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea 
Available from: 

NASA Center for AeroSpace Information 

7115 Standard Drive 

Hanover, MD 21076-1320 

443-757-5802 

Acknowledgments 

This research was partially supported under the collaborative agreement (IA1–1098) 

between NASA Langley Research Center and the Federal Highway Administration, 

Department of Transportation. The authors appreciate the assistance of Dr. Intae Bae at 

State University of New York at Binghamton for TEM sample preparation, Dr. Robert G. 

Bryant at Advanced Materials and Processing Branch, and editor Kay V. Forrest, NCI 

Information Systems, Inc., with the Research Directorate, NASA Langley Research 

Center. 

The use of trademarks or names of manufacturers in this report is for accurate re porting and does not constitute an 

official endorsement, either expressed or implied, of such products or manufacturers by the National Aeronautics 

and Space Administration.
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

v 

Abstract 

The National Aeronautics and Space Administration-invented X-ray diffraction (XRD) methods, 

including the total defect density measurement method and the spatial wafer mapping method, 

have confirmed super hetero epitaxy growth for rhombohedral single crystalline silicon 

germanium (Si1−xGex) on a c-plane sapphire substrate. However, the XRD method cannot 

observe the surface morphology or roughness because of the method’s limited resolution. 

Therefore the authors used transmission electron microscopy (TEM) with samples prepared in 

two ways, the focused ion beam (FIB) method and the tripod method to study the structure 

between Si1−xGex and sapphire substrate and Si1−xGex itself. The sample preparation for TEM 

should be as fast as possible so that the sample should contain few or no artifacts induced by the 

preparation. The standard sample preparation method of mechanical polishing often requires a 

relatively long ion milling time (several hours), which increases the probability of inducing 

defects into the sample. The TEM sampling of the Si1−xGex on sapphire is also difficult because 

of the sapphire’s high hardness and mechanical instability. The FIB method and the tripod 

method eliminate both problems when performing a cross-section TEM sampling of Si1−xGex on 

c-plane sapphire, which shows the surface morphology, the interface between film and substrate, 

and the crystal structure of the film. This paper explains the FIB sampling method and the tripod 

sampling method, and why sampling Si1−xGex, on a sapphire substrate with TEM, is necessary. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

vi 

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Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

vii 

Table of Contents 

Overview ......................................................................................................................................... 1

Focused Ion Beam Method ............................................................................................................. 3

Tripod Method ................................................................................................................................ 4

Si1–xGex on Sapphire (0001) Sample Cutting for Cross-section TEM ............................................ 4

TEM Sample Preparation of Si1–xGex on Sapphire (c-Plane, Al2O3) Substrate Using FIB ......... 5

TEM Sample Preparation of Si1–xGex on Sapphire (Al2O3) Substrate Using the Tripod Method

................................................................................................................................................... 19

Conclusion .................................................................................................................................... 27

References ..................................................................................................................................... 29

List of Figures 

Figure 1. Analysis of Si1–xGex sample. ......................................................................................... 2

Figure 2. Crystal orientation: The three grey rectangles are all equivalent. ................................ 5

Figure 3. Image of sample with silver paste on FIB holder. ........................................................ 6

Figure 4. SEM image of sample surface (top dark area: marked with a felt tip pen). ................. 6

Figure 5. Schematic diagram of FIB and SEM column position. ................................................ 7

Figure 6. Images after Pt deposition. ........................................................................................... 7

Figure 7. FIB image with regular cross-section marking. ............................................................ 8

Figure 8. Images after regular cross section. ................................................................................ 8

Figure 9. Milling the bottom side (tilt 55°) for smoothing the surface. ....................................... 9

Figure 10. Image of milling the bottom side. ................................................................................. 9

Figure 11. FIB image with a marking section for the bottom and side cuts. ............................... 10

Figure 12. Images after bottom and side cuts. .............................................................................. 10

Figure 13. Schematic image of omniprobe direction. .................................................................. 11

Figure 14. Image after inserting GIS and omniprobe. ................................................................. 11

Figure 15. Images showing that omniprobe is well aligned with the sample. ............................. 11

Figure 16. Images show Pt deposition. ........................................................................................ 12

Figure 17. Before and after cutting. ............................................................................................. 13

Figure 18. Lifting the sample. ...................................................................................................... 13

Figure 19. Image after omniprobe is moved to a safe location. ................................................... 14

Figure 20. Image of Cu-3-post grid. ............................................................................................ 14
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

viii 

Figure 21. Image after partially removing the top of TEM grid to prevent redeposition during the 

FIB sample milling. .................................................................................................... 15

Figure 22. Image after inserting the GIS near the TEM grid for attaching the sample to the grid.

..................................................................................................................................... 15

Figure 23. Image showing the sample as it is placed on top of the grid with the omniprobe. ..... 16

Figure 24. Images showing the placement of the sample. ........................................................... 16

Figure 25. The process of Pt deposition. ..................................................................................... 17

Figure 26. Image after removing omniprove from the sample. .................................................... 18

Figure 27. Performing the milling. ............................................................................................... 18

Figure 28. The sample with less than 100nm thickness. .............................................................. 19

Figure 29. Low magnification TEM image. ................................................................................ 19

Figure 30. HRTEM and its diffraction pattern result of the Si0.2Ge0.8 / sapphire interface. ......... 20

Figure 31. Cutting slices of 2.4 mm width and 4–6 mm length out of the Si1–xGex / sapphire 

wafer. .......................................................................................................................... 20

Figure 32. Mix the hardener and resin in a ratio of 1:10. ............................................................. 20

Figure 33. Schematic illustration of the forming a sandwich (stack) by slices of Si1–xGex / 

sapphire and Si dummy slices with the same level of the one side (marked by arrow).

..................................................................................................................................... 21

Figure 34. The heating process. ................................................................................................... 22

Figure 35. Coating stack with thermo-wax. ................................................................................. 22

Figure 36. Results of cutting disks with the diamond saw. ......................................................... 23

Figure 37. Diamond lapping films. .............................................................................................. 23

Figure 38. Sample mounted on tripod. ......................................................................................... 24

Figure 39. Microscope image of the TEM grid on the polished, mirror-like surface of the sample 

mounted on the Pyrex® cylinder with thermo-wax. .................................................... 25

Figure 40. Microscope image of double-side polished surface of the sample with TEM grid. ... 25

Figure 41. Ion milling system....................................................................................................... 26

Figure 42. The TEM sample on the ion milling sample holder. .................................................. 26

Figure 43. Screen shot of the ion milling setup. .......................................................................... 27

Figure 44. Low magnification TEM image after the ion milling process. .................................. 27

Figure 45. Results of the Si0.2Ge0.8 / sapphire interface. .............................................................. 28
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

ix 

Nomenclature 

Al2O3 sapphire 

C carbon 

Cu copper 

DI deionized 

EBSD electron backscatter diffraction 

FIB focused ion beam 

Ge germanium 

GIS gas injector system 

HRTEM high resolution transmission electron microscopy 

Pt platinum 

SAED selected area electron diffraction 

SEM scanning electron microscope 

Si silicon 

STEM scanning transmission electron microscopy 

TEM transmission electron microscopy 

W tungsten 

XRD X-ray diffraction 

 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

1 

Overview 

Lattice-matched Si1–xGex opens the possibility of speed improvement, compared to the single 

crystal silicon itself that has its own intrinsic limit on speed. The electron mobility of germanium 

is 4,000 cm

2

/V·s while that of silicon is only 1,400 cm

2

/V·s. The attainable speed of transistors 

made with Si1–xGex is based on the gate length and the charge mobility as related to the film 

morphology, twin structure, the number of Si1−xGex twins, and crystal structure of the Si1–xGex on 

a c-plane sapphire substrate. If the defects in Si1−xGex can be removed, Si1−xGex should allow 

faster electron motion than single crystal silicon. Transistors with higher operational frequencies 

can be fabricated for a new generation of ultrafast chipsets (among other things) for numerous 

applications. Si1−xGex on c-plane sapphire substrates also can improve the following products: 

ultrafast complementary metal oxide semiconductor chipsets; heterojunction bipolar transistors; 

thermoelectric devices; photo-voltaic solar cell devices; advanced detectors; high frequency high 

power transmitters, and so on. The National Aeronautics and Space Administration-invented Xray diffraction (XRD) methods, including the total defect density measurement method and the 

spatial wafer mapping method, confirmed super-hetero epitaxy growth for rhombohedral single 

crystal silicon-germanium (Si1−xGex) on a c-plane sapphire substrate (ref. 1 and 2). However, the 

XRD method cannot observe the surface morphology or roughness, which affects the efficiency 

of devices, because of the method’s limited resolution. For this reason, the authors have studied 

the structure between Si1−xGex and sapphire substrate, and Si1−xGex itself with transmission 

electron microscopy (TEM), and characterized the film morphology and twin structure of 

Si1−xGex thin films sputtered on sapphire (0001) substrates using cross-sectional TEM analysis. 

Figure 1 shows the differences in the results by XRD, electron backscatter diffraction (EBSD), 

and TEM of Si1–xGex thin film sputtered on sapphire (0001) substrates. The XRD wafer mapping 

method shows spatial distribution of major single crystalline Si1–xGex ( 99.9 percent) (Figure 

1a and b) and twin defect Si1–xGex ( < 0.1 percent), which coexist on the same sapphire wafer. 

The small cube icons ( and ) in Figure 1 (a) and (b) represent two possible in-plane 

azimuthal alignments inside rhombohedral alignment view from the [111] direction. The crystal 

structure of the entire wafer can be characterized with the XRD wafer mapping method. 

However, one cannot observe the surface morphology, roughness, and density of dislocation 

with the XRD method. Figure 1c shows the EBSD analysis of the crystal orientation domain in a 

small region (20 x 20 μm

2

). A few line-art cubic shapes are drawn to indicate the crystal 

orientation of each color domain with the same-colored domain having similar crystal orientation. 

The majority of the area is the blue-colored domain, a [111]-oriented majority single-crystal 

region. In XRD analysis, the ratio between a single crystal and a twin crystal was 99:1. Therefore, 

the EBSD analysis further supports the result of the XRD analysis. Currently, EBSD is the 

fastest and most reliable way in which to acquire data for crystalline structure and orientation in 

a solid crystalline phase. However, the data of EBSD are generated at very shallow depths (10 to 

20 nm) within the sample, so the cross-section TEM study is needed to confirm the crystalline 

structure and orientation of the Si1–xGex film through the thickness. Figure 1d shows the high 

resolution transmission electron microscopy (HRTEM) image of the Si1–xGex / Al2O3 (sapphire) 

interface. The orientation relationships between the Al2O3 substrate and Si1–xGex single crystal 

layer are (0001) Al2O3 || (111) Si1–xGex and [01–10] Al2O3 || [–112] Si1–xGex. The TEM results 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

2 

directly show crystal structure of the film, interface between film and substrate, and surface 

morphology. 

 

(a) Zero to 20 scan in the direction 

normal to surface with XRD. Small cube 

icons represent two possible in-plane 

azimuthal alignments inside 

rhombohedral alignment 

(b) Two inch sized X–Y wafer mapping 

with majority {440} peak showing the 

distribution of a single crystal. 

 

(c) Color-coded scanning electron 

microscope image with crystal orientation 

mapping as analyzed by EBSD. The blue 

region is the majority single crystal (111) 

domain. 

(d) HRTEM and result of the Si1–xGex / 

sapphire interface. 

Figure 1. Analysis of Si1–xGex sample. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

3 

The standard sample preparation method of mechanical polishing often requires a relatively long 

ion milling time (several hours), which increases the probability of inducing defects into the 

sample. These defects could be: 

 an ion implantation that will modify the crystal structure, 

 an amorphisation of the surface layers of the sample, 

 a possible modification of the sample chemical composition, 

 sample heating, 

 an inhomogeneity of the final thickness between the different compounds, 

 a redeposition, onto the sample’s surface of the milled materials (especially for a 

sample in plain view showing the layers on the surface and milled only from the rear 

side). 

Si1–xGex on a sapphire substrate has problems not inherent to other silicon-based materials when 

using the standard preparation method. Sapphire is a difficult material to thin because of its high 

hardness and its mechanical instability when thinned below 20μm. Delamination of Si1–xGex can 

occur during polishing or ion milling. In addition, the Si1–xGex has a markedly different ion 

milling rate than the sapphire substrate (ref. 3). Therefore, the sample preparation for the TEM 

should be completed as quickly as possible so that the sample will contain few or no artifacts 

induced by the preparation. The focused ion beam (FIB) method or a tripod polisher method 

succeeds on both counts when performing a cross-section TEM sampling of Si1−xGex on sapphire 

(0001). 

Focused Ion Beam Method 

Whereas the initial development of focus ion beam instruments was driven by their unique 

capabilities for computer chip repair and circuit modification in semiconductor technology, 

present FIB applications support a much broader range of scientific and technological disciplines 

(ref. 4). Many FIBs are largely used to prepare TEM cross-section samples (ref. 5–9). FIB 

systems operate in a similar fashion to a scanning electron microscope (SEM), except, rather 

than a beam of electrons, FIB systems use a finely focused beam of ions that can be operated at 

low beam currents for imaging or at high beam currents for site specific sputtering or milling. A 

tungsten (W) or platinum (Pt) line is deposited on the area of interest to protect the top portion of 

the sample and to mark the position of the target area. A thin slab of the material is cut from the 

area of marked interest in the sample and mechanically polished as thin as possible. The sample 

material is then mounded on a half-grid and inserted vertically into the FIB chamber where it is 

then milled. 

There are three advantages to this method. First, the target area can be precisely selected using a 

FIB scope; in that lamellae can be prepared with a spatial accuracy within ~20μm. Second, FIB 

preparation techniques are virtually independent of the nature of the material. Finally, FIB 

sample preparation can be applied to almost any material type—hard, soft, or any combination. 

The main disadvantage of FIB is the ion milling process. Here, the ion collision initiating sputter 

removal can also lead to ion implantation and cause severe damage to the remaining bulk of the 

material. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

4 

Tripod Method 

A tripod polisher, designed by scientists at IBM, was used to prepare micro sizes of TEM and 

SEM samples (ref. 10). For TEM samples, the tripod polisher has been used to limit ion milling 

times to less than 15 minutes and, in some cases, has eliminated the need for ion milling. It can 

be used to prepare both plan-view and cross-sections from a variety of sample materials, such as 

ceramics, composites, metals, and geological samples (ref. 11 and 12). The cut sample is 

mounted on the tripod polisher in order to polish the first side. This polishing is carried out with 

the change of different grain-sized diamond lapping films (30μm, 15μm, 6μm, 3μm, 1μm, 0.5μm, 

and 0.1μm). The final polishing, used to eliminate all the scratches from the surface, is carried 

out on a soft felt pad wet by a colloidal solution that contains very thin grains (0.05μm) either of 

silica, alumina, diamond, or other hard media. The sample is then removed from its support, 

turned over and reattached. The sample can be mounted on the TEM grid before polishing the 

second side. The Pyrex® cylinder (insert) has to be polished flat and level to insure the correct 

angle of the wedge shape of the sample while the opposite side is polished. Finally, the sample is 

mounted on a TEM grid with a diameter adapted to the sample holder of the ion-milling machine. 

There are many advantages utilizing this method. It allows the observation of a sample that 

cannot be ion milled. The surface obtained is of a better quality than the surface obtained with 

the mechanical polishing method. The difference in final thickness, due to the different material 

properties, between the different compounds of the sample is greatly reduced, as is the 

preparation time. Finally, this process provides the possibility of dry polishing those materials 

that cannot be polished using a lubricating fluid. The disadvantages of the tripod method are; it is 

hard to clean very large samples, it does not work well with very soft materials and may require 

some practice. 

Si1–xGex on Sapphire (0001) Sample Cutting for Cross-section TEM 

The pole piece gap of TEM equipment limits the tilting angle of sample. If the TEM sample is 

cut in the proper direction, near to the referenced zone axis, one can easily find the epitaxial 

relationship between the film and the substrate. From the X-ray diffraction data and the selected 

area electron diffraction (SAED) pattern between Si1–xGex film and sapphire substrate, the 

authors confirmed the epitaxial growth between the film and the substrate (ref. 1 and 2). The 

epitaxial relationship between the majority of the SiGe film and the sapphire substrate was found 

to be (111) Si1–xGex // (0001) sapphire and [011] Si1–xGex // [10-10] sapphire. To obtain the 

distinct diffraction patterns for two crystallographic variants rotated from each other by 60 

degrees, the TEM sample has to be tilted to SiGe <011> zone-axis orientation. This can be 

readily located by finding the [10–10] sapphire zone, which is parallel to [011] SiGe. Usually the 

(0001) sapphire substrate, that is the c-plane, with a flat {11–20} has the crystal orientation as 

shown in Figure 2. If the sample for the FIB or the tripod method is cut normal to the a1 axis as 

shown in Figure 2, one can find the [10–10] sapphire zone easily. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

5 

Figure 2. Crystal orientation: The three grey rectangles are all equivalent. 

TEM Sample Preparation of Si1–xGex on Sapphire (c-Plane, Al2O3) Substrate Using FIB 

The preparation of good TEM samples with minimum milling damage can be complicated, 

especially from a specific area in the Si1–xGex / sapphire sample. The TEM is a powerful tool for 

investigating the microstructure of materials, providing crystallographic and composition 

information at the nanometer scale. Therefore, obtaining samples that are uniform and thin (less 

than 100nm) is critical. The focused ion beam method is generally faster than other manual 

preparations and has exceedingly high placement accuracy. 

The general process using FIB for TEM sample preparation is described in several papers (ref. 

4–9). This NASA document describes specific conditions (adding the numerical value) in the 

process for sapphire sample preparation. Also, this document includes some extra tips such as 

using a felt-tip pen and cutting the TEM grid to prevent copper (Cu) redeposition during the ion 

milling. 

The complete process is as follows: 

Note: 1) Yellow marker in the figure: etching area 2) Green marker: deposition area 

1. Mount the Si1–xGex / sapphire sample on 12 mm sample holder. 

 To conduct between the sample and the sample holder, apply a silver (Ag) paste to 

prevent the buildup of an electrical charge on the sample surface (Figure 3). 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

6 

Figure 3. Image of sample with silver paste on FIB holder. 

2. Mark on the sample surface. 

 Mark the necessary indications with a felt tip pen on the surface of the sample to 

be analyzed (Figure 4). The purpose is to protect the sample surface and to 

increase the contrast. The ink of a felt tip pen is amorphous, which makes 

marking the surface much easier and cheaper than the sputtering method. After 

drying the sample, coat the sample surface with a conducting material if the 

sample is composed of a non-conducting material. 

Figure 4. SEM image of sample surface (top dark area: marked with a felt tip pen). 

3. Mount the sample holder in a FIB (FEITM Company, QuantaTM 3D FEG) chamber. 

(1) Evacuate the main chamber. 

(2) Turn on beams, the SEM column and ion column. 

(3) Move the sample stage to the location where the fabrication is to be done. 

(4) After focusing the sample surface with the SEM, raise the holder to about 

Z = 10mm to adjust the eucentric height of the sample to a 0 degree angle. Repeat 

but adjust the angle by 7, 15, and 52 degrees, respectively. This is because the 

Felt tip pen 

Unmarked 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

7 

FIB column has a different angle to the SEM column by 52 degrees. The 0 degree 

angle means that the sample is located vertically to the SEM column and 38 

degrees to the FIB column. So, if that sample is to be faced vertically with the FIB 

column, it should be tilted by 52 degrees. For the same eucentric height, both in 

the SEM and the FIB mode, repeat the adjustment for the same location by 7, 15, 

and 52 degrees, respectively (Figure 5). 

Figure 5. Schematic diagram of FIB and SEM column position. 

4. Perform e-beam deposition of Pt (tilt 0 degrees). 

 Put a platinum line on the area of interest to protect the top portion of the sample 

and to mark the position of the target area. (If step 2 has been completed, skip this 

step.) 

 SEM condition: 2kV, 0.47nA, X = 12μm, Y = 2μm, with a duration of 3 minutes 

5. Perform ion deposition of Pt (tilt 52 degrees) (Figure 6). 

 Ion condition: 30kV, 0.3nA, X = 12μm, Y = 2μm, Z = 1.5μm, with duration 3 to 5 

minutes. 

(a) Tilted view SEM image. (b) Top-view FIB image. 

Figure 6. Images after Pt deposition. 

Pt deposition line Pt deposition line 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

8 

6. Cut the sample. 

 Select the mode “Regular Cross Section (making a regular cross section),” which 

will work quickly and will roughly make the sample the shape of a “step” (Figure 

7). 

 Cut the sample in ion condition: 30kV, 30nA, X = 24μm, Y = 18μm, Z = 8μm, with 

a duration of 14 minutes. 

 Figure 8 shows the images after regular cross section. 

Figure 7. FIB image with regular cross-section marking. 

 

(a) Tilted view with SEM image. (b) Top view with FIB image.

Figure 8. Images after cutting out cross-sectional areas (Fig. 7).

Area for 

cutting 

After the 

cutting 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

9 

 Tilt the sample by ±3 degrees, 55 degrees for milling the bottom side and 49 

degrees for milling the top side (Figure 9). 

 Select the mode “Rectangular (30kV, 5nA).” This mode has the same etching rate 

in the yellow box (Figure 9) so the etched section of sample can be clean and 

smooth (Figure 10b). 

Figure 9. Milling the bottom side (tilt 55°) for smoothing the surface. 

 

(a) Image before milling the sample. (b) Image after milling the sample. 

Figure 10. Image of milling the bottom side.

 Do a scan rotation (“Ion image”) by 180 degrees. (This is to correct the ion image 

displayed upside down from (a) to (b) in Figure 11.) (keyboard shortcut for scan 

rotation : shift + F12) 

 Select the mode “Rectangular (30kV, 5nA, tilt = 0°)” as shown in Figure 11 for 

cutting the bottom and side walls. 

 Continue until the etched line is visible on the opposite surface with the SEM 

image as a reference (Figure 12). 

Area for cutting 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

10 

 

(a) Before 180° scan rotation (b) After 180° scan rotation 

Figure 11. FIB image with a marking section for the bottom and side cuts. 

 

(a) Top view SEM image after cutting. (b) Tilted view FIB image.(Already 180°

scan rotation done in Figure 11) 

Figure 12. Images after bottom and side cuts. 

7. Lift up the sample using the omniprobe. 

 Figure 13 shows the omniprobe direction in the SEM and FIB modes. When 

looking at the SEM image, one can control the X and Z axes. Also, one can 

control the Y and Z axes in FIB mode. 

 Insert the omniprobe and gas injector system (GIS) for using Pt at tilt = 0° (Figure 

14 and Figure 15). 

 

Area for cutting 

After the 

cutting 

After the 

cutting 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

11 

(a) The SEM image. (b) The ion image. 

Figure 13. Schematic image of omniprobe direction. 

Figure 14. Image after inserting GIS and omniprobe.

 

 (a) Top view of SEM image. (b) Side view FIB image. 

Figure 15. Images showing that omniprobe is well aligned with the sample. 

Omniprobe 

omniprobe 

omniprobe 

GIS 

(Gas Injection System) 

omniprobe 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

12 

 The process of attaching the probe to the sample by Pt deposition is performed 

with the condition: 30kV, 0.1nA, X = 1.69μm, Y = 4.09μm, Z = 1.0μm using Pt gas 

for 2 minutes (Figure 16). 

 

 (a) Top view SEM image. (b) Tilted view FIB image with the 

marking for Pt deposition. 

 

(c) Tilted view FIB image after deposition. (d) Top view SEM image of figure (c) 

after Pt deposition.

Figure 16. Images show Pt deposition. 

 Cut the remaining side wall of the sample (30kV, 5nA) as shown in Figure 17. 

Area for Pt 

deposition 

Pt Pt 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

13 

 (a) FIB image with a marking for 

cutting the remaining side of the 

sample. 

 (b) FIB image after cutting the side. 

Figure 17. Before and after cutting. 

 Lower the stage carefully after cutting the remaining side wall (Figure 18). 

 Move omniprobe to a safe location, the proper place that sample and stage don’t 

collide with each other when stage moves. (Figure 19). 

 (a) FIB image. (b) Low magnification FIB image. 

Figure 18. Lifting the sample. 

Area for 

cutting 

Cut 

area 

Lower the stage 

Relatively TEM 

sample moves upward 

TEM sample 

TEM sample 

Area to be cut 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

14 

Figure 19. Image after omniprobe is moved to a safe location. 

 Remove omniprobe and GIS (Figure 19). Move the stage to the place where the 

grid is located to attach the sample to the grid (Figure 20). 

Figure 20. Image of Cu-3-post grid. 

8. Remove a part of the top of the grid to prevent Cu redeposition from grid when milling 

the sample using ion-beam. 

 The etching width should be less than the lateral width of the sample (Figure 21). 

TEM Cu grid 

Sample 

Omniprobe 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

15 

 

(a) Top view Fig. 20. (b) Side view Fig. 21a. 

Figure 21. Image after partially removing the top of TEM grid to prevent redeposition 

during the FIB sample milling. 

 To attach the sample to the grid, insert the omniprobe and GIS (Pt) (Figure 22). 

Figure 22. Image after inserting the GIS near the TEM grid for attaching the sample to the 

grid. 

9. Mount the cut sample on top of the grid using the omniprobe (Figure 23). 

TEM Cu grid 

Zoom-in view Figure 20 

GIS 

(Gas Injection System) 

TEM Cu grid 

TEM Cu grid 

Zoom-out side view 

Figure 21(a) 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

16 

Figure 23. Image showing the sample as it is placed on top of the grid with the omniprobe. 

 Locate the sample about 1 to 2μm above the grid to facilitate deposition (Figure 

24). 

 (a) The sample near the top of the 

grid. 

 (b) The sample about 1 to 2μm

above the grid. 

Figure 24. Images showing the placement of the sample. 

 Attach the sample to the grid by deposition (30kV, 0.1nA, X = 3.40μm, Y = 2.10μm, 

Z = 1.00μm using Pt gas for 2 to 3 min). Figure 25 shows the process. 

TEM Cu grid 

TEM sample 

omniprobe 

TEM Cu grid 

omniprobe 

GIS 

Align the 

sample(dash line) 

and then down it 

about 1 to 2um 

above the grid 

Move the sample 

to the cut area 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

17

 

(a) Sample well aligned with the TEM grid. (b) Markings on the sample for Pt

deposition to attach the sample to the grid. 

(c) After Pt deposition. 

Figure 25. The process of Pt deposition. 

 Remove the omniprobe from the sample by cutting the connection between the 

sample and omniprobe (30kV, 1nA for 2 min) (Figure 26). 

Area for Pt deposition 

omniprobe 

TEM Cu 

grid 

TEM sample 

Pt Pt 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

18

Figure 26. Image after removing omniprove from the sample. 

 Move the omniprobe to a safe location. To do the final milling, the tilt = 52°. 

After tilting the sample ±1.3 degrees (for top side : 53.3 and for bottom side : 50.7 

degrees), perform the milling at 30kV, 1nA. Continue until the thickness of the 

sample comes into the range of 200 to 300nm (Figure 27). 

 

 (a) Top view FIB image. (b) SEM image. 

Figure 27. Performing the milling. 

 After tilting ±0.8 degrees (for top side : 52.8 and for bottom side : 51.2 degrees), 

perform the milling at 30kV, 100pA. Continue until the thickness comes into the 

range of 40 to 70nm (Figure 28). 

Area for milling 

Step by step

Cutting the connection 

Side view Figure 27(a) 

TEM Cu grid

omniprobe
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

19

 

(a) FIB image. (b) SEM image. 

Figure 28. The sample with less than 100nm thickness. 

 Figure 29 shows the TEM low magnification image after making the sample using 

FIB. 

Figure 29. Low magnification TEM image. 

 From the SAED pattern, the epitaxial relationship between the majority of SiGe

film and sapphire substrate was found to be (111) Si0.2Ge 0.8 // (0001) sapphire and 

[-112] Si0.2Ge0.8 // [01–10] sapphire (Figure 30). 

Step by step 

TEM grid

TEM sample 

Side view Figure 28(a) 

As the thickness of 

sample is thinner, Top 

area is apt to be 

damaged by Ga ion 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate 20

20

 (a) HRTEM. (b) Diffraction pattern result. 

Figure 30. HRTEM and its diffraction pattern result of the Si0.2Ge0.8 / sapphire interface. 

TEM Sample Preparation of Si1–xGex on Sapphire (Al2O3) Substrate Using the Tripod 

Method 

The use of the tripod allows the polishing of the sample to be faster than with the traditional 

preparation, with the resulting image being of higher quality. The total sample preparation time 

was approximately 3 hours, with the ion milling comprising over half of the time. 

1. Prepare the sample. 

 Cut slices of the Si1–xGex / sapphire into samples, each nor greater than 2.4 mm 

width (for a 3 mm slotted grid) and 4–6 mm length along the [01–10] directions 

(Figure 31). 

Figure 31. Cutting slices of 2.4 mm width and 4–6 mm length out of the Si1–xGex / sapphire 

wafer. 

Si1-xGex / sapphire samples 

2.4mm 4-6mm
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

21

 Clean the pieces with deionized (DI) water, acetone, and iso-propanol, then put 

the pieces on a hot plate at 100 degrees Celsius (C) to evaporate any solvent 

residue. 

2. Prepare the stack. 

 Prepare the epoxy. Using G1 from Gatan which permits a very thin film of glue 

and becomes very hard after the polymerization. It is also relatively stable under 

the electron beam. 

 The standard ratio between the hardener and the resin of G1 is 1:10 (Figure 32). 

At 120 degrees C, the hardening time is about 10 minutes. A good way to find out 

when the epoxy glue has hardened is to put a small drop of epoxy next to the 

stack on the hot plate. The color of the epoxy will change from transparent yellow 

to brown when it is fully hardened. 

Figure 32. Mix the hardener and resin in a ratio of 1:10. 

 Spread the glue on a smooth, clean surface with a wooden toothpick. Place the 

mating surfaces of the sandwich on the glue, taking care to obtain a very thin film 

of glue (Figure 33). 

 

Figure 33. Schematic illustration of the forming a sandwich (stack) by slices of Si1–xGex / 

sapphire and Si dummy slices with the same level of the one side (marked by arrow). 

Hardener

Resin
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

22

 Stick the cutting pieces of the Si1–xGex / sapphire together, taking care that at least 

one side at each end is at the same level. A Si wafer dummy is needed for the 

front and back sides of the sapphire wafer since the sapphire wafer is transparent, 

one cannot estimate the thickness after polishing. The attached Si dummy wafer is 

used to measure the polishing rate. 

 Place the stack in a press using two Teflon® adhesive sheets to prevent the sample 

from being glued to the press. 

 Heat the stack in the clamping fixture for a minimum of 10 minutes (Figure 34). 

 

(a) Clamping fixture with 

Teflon® adhesive sheets. 

(b) Stack in a clamping 

fixture on hot plate at 

120°C. 

(c) The clamping fixture 

heated for 10 minutes at 

120°C. 

Figure 34. The heating process. 

3. Mount the sample on the tripod. 

 Place the glass on a hot plate (120 °C). Once the glue is liquefied, attach the 

sample on the glass with a QuickStickTM 135 Temporary Mounting Wax, used to 

bond samples during processing (Figure 35). 

 (a) Applying thermo-wax. (b) Slide on a hot plate. (c) Stack with thermo-wax 

on the glass. 

Figure 35. Coating stack with thermo-wax. 

 When the thermo-wax liquefies (after a few seconds on the hot plate), the stack 

will sink into the QuickStickTM 135 Temporary Mounting Wax (thermo-wax). If 

Thermo-wax
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

23

the stack does not sink into the thermo-wax, apply a small amount of pressure on 

the stack. 

 Attach the glass, with the thermo-wax covered stack, to the aluminum holder. 

Using a diamond saw, cut disks of about 300–400 μm thickness (Figure 36). 

Apply the thermo-wax all around the glass when mounting it on the Al holder to 

ensure adhesion between the two. The speed of the diamond saw should be kept 

low. 

 (a) Mounted on the 

diamond saw. 

(b) Disks of about 300–400 μm

thickness. 

(c) Disk under the microscope. 

Figure 36. Results of cutting disks with the diamond saw. 

4. Polish the sample. 

 Lay down the 35μm diamond lapping film (Figure 37) on the wet polishing 

machine plate and remove the water from between the polishing plate and the 

lapping film using a squeegee until the lapping film adheres completely to the 

plate. 

Figure 37. Diamond lapping films. 

 Select a Pyrex® cylinder to use as a support for the disk, and measure its height 

with a micrometer. 

 Attach one disk with thermo-wax on top of the Pyrex® cylinder. 

Mount the Pyrex® cylinder with the stack sample (disk) in the tripod ( 

 Figure 38). 

Si1-xGex / sapphire 

Silicon 

Stack on glass from 

Figure 35 (c) 

Diamond saw 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

24

 (a) Pyrex® cylinder to 

use as a support for the 

disk. 

(b) Attached disk with 

thermo-wax on top of the 

Pyrex® cylinder. 

(c) The Pyrex® cylinder with the 

stack sample mounted on the 

tripod. 

Figure 38. Sample mounted on tripod. 

 Put the tripod on the disc by placing the rear micrometers on it and gently 

lowering the sample, keeping the glue-line parallel to the direction of motion. 

 Polish the sample in a spiral motion from inside to outside with the 35μm

diamond lapping film until the entire face of each of the two pieces is abraded. 

This can be seen by the homogeneity of the scratches induced on the surface of 

the sample. Take care not to use the same area of the lapping film more than once. 

When the whole surface of the film has been used, clean it with a wet, lint free 

paper towel. 

 Measure the thickness of the sample either by using the focus indicator of the 

microscope or by installing a digital thickness indicator on the microscope. Use 

the attached Si dummy wafer to measure the polishing rate since the sapphire 

wafer is transparent. 

5. Glue the TEM grid on the TEM sample and polish the second side (Figure 39 and Figure 

40). 

 Glue the TEM grid on the polished, mirror-like surface of the sample. Mount the 

sample with thermo-wax on the Pyrex® cylinder of the tripod for polishing the 

second side. Adjust the two rear micrometers to obtain the desired angle. 

 For the second side, measuring the thickness of the sample is very important and 

must be done periodically (once every 20 seconds). This is carried out using an 

optical microscope with the Si dummy samples. Polish with a 35μm and 30μm

diamond lapping film until the the sample is 170μm thick. Polish parallel to the 

glue line, the thin zone being at the tapered corner. 

 Polish with a 15μm diamond lapping film until the thickness is 80μm. 

 Polish with a 6μm diamond lapping film until the thickness is 30μm. 

 Polish with a 3μm diamond lapping film until the thickness is about 10μm. 

 Polish with a 1μ, 0.5μ, and 0.1μm diamond lapping film until the appearance of 

interface fringes at the side of the sample. 

TEM disk

Tripod 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

25

Figure 39. Microscope image of the TEM grid on the polished, mirror-like surface of the 

sample mounted on the Pyrex® cylinder with thermo-wax. 

Figure 40. Microscope image of double-side polished surface of the sample with TEM grid. 

6. Clean the sample. 

 Clean the sample mounted to the TEM grid with acetone, followed by an ethanol 

or trichlorethylene bath (all solvent must be of analysis quality) to remove the 

thermo-wax from the sample and separate the sample from the Pyrex® cylinder. 

Put the TEM sample on a hot plate at 100 °C to evaporate the solvent residue. 

7. Ion milling the sample (Figure 41). 

 A low angle ion milling and polishing system (Fischione Instrument Model 1010), 

was used for the ion milling process. The parameters for the ion milling process 

are rather specific for each material and have to be optimized. As ion milling rate 

increases with a higher etching angle and higher etching voltage; the sample is 

more severely damaged. Therefore, the angle, as well as the voltage, should be 

kept rather low. Generally, a higher voltage combined with a lower angle is less 

harmful to the sample than a lower voltage combined with a higher angle. 

 Add liquid nitrogen to cool the ion miller since the sample becomes severely 

heated during ion milling. 

Pyrex® cylinder 

TEM disk

TEM grid

Pyrex® cylinder 

Double-side 

polished TEM disk 

TEM grid
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

26

 (a) A low angle ion milling and polishing 

system for the ion milling process. 

(b) Liquid nitrogen sample cooling 

to eliminate artifacts. 

Figure 41. Ion milling system. 

 Mount the polished sample (TEM sample) on the ion milling sample holder 

(Figure 42). 

Figure 42. The TEM sample on the ion milling sample holder. 

 Make sure that the ion milling machine is turned on approximately 1 hour before 

beginning the ion milling in order for it to reach stable, high-vacuum conditions. 

 Mount the sample holder into the milling machine. 

 Close the cover and create a vacuum of the chamber. 

 Set the turning velocity, ion milling angle, ion milling voltage, and duration of the 

ion milling. 

 Start the ion milling process (Figure 43). 

TEM sample with grid
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

27

Figure 43. Screen shot of the ion milling setup. 

8. Finalize the TEM sample (Figure 44 and Figure 45). 

 A TEM sample is least contaminated directly after the ion milling process. If 

necessary, you can remove some contamination by the short plasma-clean prior to 

the TEM investigation. 

 From the diffraction pattern, the epitaxial relationship between the majority of the 

SiGe film and the sapphire substrate was found to be (111) Si0.2Ge 0.8 // (0001) 

sapphire and [–112] Si0.2Ge 0.8 // [01-10] sapphire. 

Figure 44. Low magnification TEM image after the ion milling process. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

28

 (a) HRTEM. (b) SAED pattern. 

Figure 45. Results of the Si0.2Ge0.8 / sapphire interface. 

Conclusion 

In high resolution transmission electron microscopy, the quality of the TEM samples becomes a 

limitation factor, and, with the realization of aberration corrected TEMs, this effect is more 

prominent. Thus, it is crucial that the preparation does not cause any degradation of a sample 

used in a TEM study. The conventional argon-ion milling scheme can leave an amorphous 

surface layer on the sample with a thickness up to 10 nm. Such alteration leads to a deterioration 

of the electron channeling along atom columns and, hence, a decreased contrast in atomic 

resolution scanning TEM. The preparation of a TEM sample should be as fast as possible, and 

the specimen should contain few or no artifacts induced by the preparation. The standard sample 

preparation method of mechanical polishing often requires a relatively long ion milling time, 

which increases the probability of inducing defects into the sample and the amorphous layer on 

the surface of the sample. Promising approaches are to apply the FIB and tripod polishing 

methods in the sample preparation procedure. The use of the FIB or tripod methods allows faster 

polishing of the sample than with traditional preparation and obtains excellent image quality as 

well. 
Transmission Electron Microscopy (TEM) Sample Preparation of Si1–xGex in c-Plane Sapphire Substrate

29

References 

1. Park, Yeonjoon, King, Glen C., and Choi, Sang H., “Rhombohedral Epitaxy of Cubic SiGe

on Trigonal c-Plane Sapphire,” Journal of Crystal Growth, Vol. 310, No. 11, pp. 2724–

2731, 15 May 2008. 

2. Kim, Hyun-Jung, Bae, Hyung-Bin, Park, Yeonjoon, Lee, Kunik, and Choi, Sang H., 

“Temperature dependence of crystalline SiGe growth on sapphire (0001) substrates by 

sputtering,” Journal of Crystal Growth, Vol. 353 (1), pp. 124-128, 2012 

3. Chen, J. and Ivey, D. G., “Preparation of Metallized GaN / Sapphire Cross Section for 

TEM Analysis Using Wedge Polishing,” Micron, Vol. 33, No. 5, pp. 489–492, 2002. 

4. Giannuzzi, L. A., Stevie, F. A., editors, Introduction to Focused Ion Beams: 

Instrumentation, Theory, Techniques, and Practice, Springer Science + Business Media, 

Inc., New York, 2005. 

5. Mayer, J., Giannuzzi, L. A., Kamino, T., and Michael, J., “TEM Sample Preparation and 

FIB-induced Damage,” MRS Bulletin, Vol. 32, pp. 400–407, May 2007. 

6. Kirk, E. C. G., Williams, D. A., and Ahmed, H., “Cross-sectional Transmission Electron 

Microscopy of Precisely Selected Regions from Semiconductor Devices,” Institute of 

Physics Conference Series 100, pp. 501–506, 1989. 

7. Basile, David P., Boylan, Ron, Baker, Brian, Hayes, Kathy, and Soza, David, “Fibxtem – 

Focused Ion Beam Milling for TEM Sample Preparation,” 1991 Materials Research 

Society Fall Meeting, Materials Research Society Proceedings, Vol. 254, pp. 23–42, 

January 1991, doi:10.1557/PROC–254–23. 

8. Overwikj, M. H. F., van den Heuvel, F. C., Bull-Lieuwma, C. W. T., “Novel Scheme for 

the Preparation of Transmission Electron Microscopy Specimens with a Focused Ion 

Beam,” Journal of Vacuum Science and Technology B, Vol. 11, No. 6, 2021–2024, 1993, 

http:\\dx.doi.org/10.1116/1.586637, Accessed on 16 May 2012. 

9. Giannuzzi, L. A., Drown, J. L., Brown, S. R., Irwin, R. B., and Stevie, F. A., “Focused Ion 

Beam Milling and Micromanipulation Lift-Out for Site Specific Cross-Section TEM 

Specimen Preparation,” 1997 Materials Research Society Spring Meeting, Materials 

Research Society Proceedings, Vol. 480, pp. 19–28, January 1997, doi:10.1557/PROC–

480–19. 

10. Klepeis, S. J., Benedict, J. P., Anderson, R. M., “A Grinding/Polishing Tool for TEM 

Sample Preparation,” 1987 Materials Research Society Fall Meeting, Materials Research 

Society Proceeding, Vol. 115, pp. 179-184, September 1988, doi:10.1557/PROC-115-179. 

11. Benedict, J. P., Anderson, Ron, Klepeis, S. J., Chaker, M., “A Procedure for Cross 

Sectioning Specific Semiconductor Devices for Both SEM and TEM Analysis,” Ed. R. 

Anderson, 1990 Spring Meeting, MRS Proceeding 1990 199:189, Cambridge University 

Press, http://dx.doi.org/10.1557/PROC-199-189, Accessed 16 May 2012. 

12. Sridhara Rao, D. V., Muraleedharan, K., and Hymphreys, C. J., “TEM Specimen 

Preparation Techniques,” Microscopy: Science, Technology, Applications and Education, 

FORMATEX Microscopy Series No. 4, Vol. 3, pp. 1232–1244, 2010. 
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 4. TITLE AND SUBTITLE

Transmission Electron Microscopy (TEM) Sample Preparation of Si1-xGex 

in c-Plane Sapphire Substrate 

5a. CONTRACT NUMBER

 6. AUTHOR(S)

Kim, Hyun Jung; Choi, Sang, H.; Bae, Hung-Bin; Lee, Tae Woo

 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)

NASA Langley Research Center

Hampton, VA 23681-2199

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National Aeronautics and Space Administration

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14. ABSTRACT

The National Aeronautics and Space Administration-invented X-ray diffraction (XRD) methods, including the total defect density measurement method and 

the spatial wafer mapping method, have confirmed super hetero epitaxy growth for rhombohedral single crystalline silicon germanium (Si1-xGex) on a c-plane 

sapphire substrate. However, the XRD method cannot observe the surface morphology or roughness because of the method’s limited resolution. Therefore the 

authors used transmission electron microscopy (TEM) with samples prepared in two ways, the focused ion beam (FIB) method and the tripod method to study 

the structure between Si1-xGex and sapphire substrate and Si1-xGex itself. The sample preparation for TEM should be as fast as possible so that the sample 

should contain few or no artifacts induced by the preparation. The standard sample preparation method of mechanical polishing often requires a relatively long 

ion milling time (several hours), which increases the probability of inducing defects into the sample. The TEM sampling of the Si1-xGex on sapphire is also 

difficult because of the sapphire’s high hardness and mechanical instability. The FIB method and the tripod method eliminate both problems when performing 

a cross-section TEM sampling of Si1-xGex on c-plane sapphire, which shows the surface morphology, the interface between film and substrate, and the crystal 

structure of the film. This paper explains the FIB sampling method and the tripod sampling method, and why sampling Si1-xGex, on a sapphire substrate with 

TEM, is necessary. 

15. SUBJECT TERMS

Focused ion beam; Sapphire; Substrates; Transmission electron microscopy; Tripod

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