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1. Sample Preparation for Resist Coating
Note: In this work, patterns with single-digit nanometer resolution are defined in PMMA (positive- and negative-tone) and HSQ resists, which are spin-cast onto commercially available TEM windows (approximately 50 µm x 50 µm) with SiNx or SiO2 membranes with thicknesses ranging from 5 nm to 50 nm. One or more TEM windows are fabricated in a 3-mm diameter silicon handling frame (100 µm thick). Throughout this manuscript, we refer to the whole unit as the TEM chip and to the electron-beam transparent membrane as the TEM window.
- Remove any organic residue from the TEM chip by performing O2 plasma cleaning for 30 s at 100 W (chamber pressure of 230 mT at approximately 5 sccm O2 flow).
- Cleave a piece of silicon wafer, approximately 2 cm x 2 cm in size, to use as a holder for the TEM chip during resist spinning.
- Place two stripes of double-sided carbon tape approximately equidistant from the center of the silicon holder and separated slightly less than the diameter of the TEM chip (see Figure 1). Rinse the stripes with isopropyl alcohol (IPA) to reduce their adhesive strength. This is necessary to avoid breaking the delicate TEM chip during removal from the Si holder.
- Mount the TEM chip on the silicon holder making sure that it is attached to the carbon tape stripes only at two opposite edges as shown in Figure 1.

Figure 1: TEM chip holder for resist spinning. Notice that the TEM chip is attached to the silicon holder only at two edges to diminish the surface area contact, and hence, the adhesion force. Please click here to view a larger version of this figure.
2. Spin Coat Parameters for PMMA (Positive and Negative Tone) and HSQ Resists
Note: Resist thickness is not measured directly on the TEM chip, since it is small and usually the resist is cast on other thin layers (e.g., Si film on SiO2 membrane), which complicates the measurement. Instead, resist thickness is determined by the spin speed calibrated using reflectometry measurements from films cast on a bulk Si sample. Reflectometry results were corroborated, usually with a precision better than 20%, by STEM top-down images of collapsed structures.
- Mount the silicon holder on the spinner chuck and align the center of the TEM window approximately with the center of the spinner rotor.
- Using a pipette, cover the entire TEM window with one drop (approximately 0.05 mL) of PMMA (A2 950K PMMA diluted in anisole to 0.5-1.0%) or HSQ (1% solids XR-1541).
- Depending on the resist used, follow the spin coating and baking parameters shown in Table 1.
- Carefully remove the TEM chip from the silicon holder. Inspect the resist uniformity over the TEM window using an optical microscope. If the film is homogenous across the central region of the membrane, proceed to the next step; otherwise, repeat the resist coating process on a fresh TEM window.
| Resist | Spin speed
(x g) | Film
Thickness
(nm) | Baking temperature
(°C) | Baking time
(min) |
| Positive-tone PMMA | 60 | 30 | 200a | 2a |
| Negative-tone PMMA | 60 | 15 | 200a | 2a |
| HSQ | 107 | 10 | Not neededb | Not neededb |
| asee Ref.12; bsee Ref. 13 |
Table 1: Resist spin coating and baking parameters. Spin speed units in x g consider a 3-mm diameter TEM chip. Baking is performed on a hot plate for PMMA. No baking is needed for HSQ13. HSQ resist is stored refrigerated, so it needs to warm up to room temperature before spinning.
3. Load Sample in STEM, Map Window Coordinates, and Perform High-Resolution Focusing
- Mount the resist-coated TEM chip on the STEM sample holder, making sure that the resist-vacuum interface faces the incoming beam, since the beam is optimally focused at the top of the sample. Also, make sure that the sides of the TEM window are aligned approximately with the x- and y-axis of the STEM stage. This will facilitate navigating to the TEM window.
- Load the TEM chip into the microscope, and pump overnight to reduce contaminants in the sample chamber.
- Move the stage (x, y) coordinates such that the beam is more than 100 µm away from the center of the TEM window (to avoid accidental exposure). Set the STEM probe beam current and energy to 34 pA and 200 keV, respectively.
- In diffraction mode imaging (stationary beam, z-contrast mode and mid-angle annular dark-field detector), set magnification to 30 kX with the beam out of focus, which makes it easier to find an edge of the TEM window.
NOTE: The TEM window edges can also be found in imaging mode. We use diffraction mode because it is faster, since the beam does not need to be scanned to form an image.
- Navigate towards the TEM window until an edge of the window is observed on the diffraction image. Navigate along the window edges and record the (x, y) coordinates of the four corners of the TEM window.
- At the last window corner, increase magnification to 50 kX and perform rough focusing on the window membrane by moving the stage z-coordinate (z-height adjustment) until the crossover of the diffraction pattern orientation is observed. Subsequently, perform fine focusing by adjusting the objective lens current.
- Increase magnification to 180 kX. Adjust focus, stigmation and aberration correction settings in order to obtain an aberration-corrected diffraction image of the window membrane as shown in Figure 2B. This focusing method is known as the Ronchigram method14.

Figure 2: Diffraction image of TEM window membrane. (A) Focused but stigmatic image. The aberration-correction settings for this image are not optimum as evidenced by the closely-spaced diffraction fringes. (B) Exposure-ready non-stigmated image showing a smooth plateau diffraction pattern. Please click here to view a larger version of this figure.
4. Expose Patterns Using an Aberration-Corrected STEM Equipped with a Pattern Generator System.
Note: The aberration-corrected STEM used in this work is equipped with a pattern generator system (PGS), which controls the electron-beam position to expose patterns defined using computer aided design (CAD) software. Dose is controlled by defining the spacing between exposure points (step size) and the exposure time per point. Table 2 summarizes the exposure parameters used in this protocol. Patterns are exposed at the center of the TEM window in "continuous mode," since the STEM used in this work does not include a beam blanker. Before and after the exposure, PGS positions the beam at any user-defined point in the field of view (FOV), preferably away from the pattern area. We use in this protocol the top right and bottom right corners of the FOV as the initial and final beam positions, respectively.
| Resist | Dot exposure | Line exposure | Area exposure |
Dose
(fC/dot) | Step size
(nm) | Dose
(nC/cm) | Step size
(nm) | Dose
(µC/cm2) |
| Positive tone PMMA | 10-100 | 0.5 | 2–8 | 0.5 | 2,000 |
| Negative tone PMMA | 50-500 | 0.5 | 20–40 | 0.5 | 50,000–80,000 |
| HSQ | 10-100 | 0.5 | 10–20 | 0.5 | 20,000–30,000 |
Table 2: Exposure parameters for PMMA (positive and negative tone) and HSQ resists. The values shown are generic, since optimal dose values depend on the specific pattern design and targeted feature dimensions.
- Close the beam gate valve to avoid any accidental exposure of the resist when moving the stage. Verify that the beam current is 34 pA and magnification is 180 kX.
- Use the pre-recorded window corner coordinates to move the stage, so that the FOV center is 5 µm away from the center of the window. Open the beam gate valve and focus at this point using the Ronchigram method described in Step 3.6.
- Close the beam gate valve. Move the stage to place the FOV at the center of the TEM window. Change magnification to 18 kX (corresponding to a 5 µm x 5 µm patterning FOV). Transfer the beam control to PGS and position the beam anywhere away from the pattern area (we use the top right corner in this protocol).
- Perform the following actions in quick succession to avoid overexposing the resist at the initial and final beam positions.
- Open the gate valve and verify, by observing the beam diffraction pattern image, whether the beam is in focus at the initial beam position (as in Figure 2B). Expose the pattern.
- When the exposure is complete, check if the diffraction pattern image remains in focus at the final beam position. Finally, close the gate valve.
- Remove the TEM chip from the STEM.
5. Resist Development and Critical Point Drying
Note: The development process depends on the resist used. Steps 5.1, 5.2, and 5.3 describe the developing process for positive-tone PMMA, negative-tone PMMA, and HSQ, respectively. However, all resists share the same final critical point drying process, which is necessary to avoid pattern collapse due to the high-aspect ratio of the patterns fabricated with this protocol. Critical point drying (CPD) uses liquid CO2 as working fluid, which is not miscible with water. Consequently, sample dehydration (steps 5.4-5.7) require the use of ACS reagent grade isopropyl alcohol (IPA).
- Developing of positive-tone PMMA15: Prepare a 100-mL beaker with 3:1 solution of IPA:methyl isobutyl-ketone (MIBK). Place the beaker in a bath circulator at 0 °C (an ice bath at 0 °C is a lower cost alternative) and wait until the temperature is equalized. Grab the TEM chip with a pair of tweezers and gently stir it in the cold solution for 30 s. Proceed with Step 5.4.
- Developing of negative-tone PMMA16: Gently stir the TEM chip in MIBK at room temperature (24 °C) for 2 min. Transfer the sample to an acetone solution and stir for 3 min. Proceed with step 5.4.
- Developing of HSQ13: Stir the TEM chip in a "salty" deionized water solution, containing 1 wt% NaOH and 4 wt% NaCl, for 4 min at 24 °C. Stir the chip in pure deionized water for 2 min (to rinse off the salty developer). Proceed with Step 5.4.
- Dip the TEM chip in ACS reagent grade IPA and gently stir it for 30 s.
- Quickly place the TEM chip on the special 2" Si wafer shown in Figure 3A. Make sure that the TEM chip is always wet with IPA during the transfer. After approximately 2-3 min, close the CPD wafer holder assembly as depicted in Figure 3B. Leave the whole unit soaking in ACS reagent grade IPA for additional 15 min totally immersed in IPA.
- Quickly transfer the complete CPD wafer holder assembly to a second container with fresh ACS reagent grade IPA and leave it for 15 min totally immersed in IPA.
- Transfer the CPD wafer holder assembly to the CPD instrument process chamber (at all times the TEM chip should be totally immersed in IPA). Run the CPD process following the instrument's operating instructions.

Figure 3: In-house solution for the dehydration of TEM chips in a CPD standard 2" wafer holder. (A) Schematic side view of the TEM chip on a special 2" Si wafer with a small hole drilled in the center (approximately 500 μm in diameter) to allow liquid flow. The wafer fits in a CPD standard 2" wafer holder supplied by the CPD system manufacturer. (B) A second special Si wafer encloses the TEM chip, thus reducing turbulent flow during the CPD process. In A and B, the CPD wafer holder is totally immersed in ACS reagent grade IPA. Please click here to view a larger version of this figure.