Table 1 |.

Troubleshooting table

Step	Problem	Possible reason	Solution
Resin preparation (REAGENTS SETUP)	Micro-nanobubbles formation (Supplementary Fig. 1)	Air trapped in the resin	Remove bubbles by placing the resin container in a vacuum chamber
34	Missing Cr masks (Supplementary Fig. 2)	Excessive sonication or unclean surface of the substrate pieces that makes Cr attachment to the substrate less firm	The initial cleaning of the substrate must be thorough and the substrate should be carefully checked to make sure there is no stain left in the region to pattern. In the sonication process of lift-off, the chip should be frequently checked
43	Collapse of nanostructures (Supplementary Fig. 9)	Undercut due to the heat built up at the bottom of the nanostructures	Make the heat transfer from chip to the wafer holder sufficient. Ensure the surface of the holder is clean, and apply vacuum pump oil between chip and wafer holder to facilitate the heat transfer
S59	Poor cell attachment	Inappropriate surface treatment method	First, choose a chemical (such as collagen and gelatin) that effective attaches the cells of interest. Interactions between surface chemistry and cells largely vary, so it is advised to learn from references. Second, utilize a surface treatment approach that effectively immobilize the chemical for attaching cells. Covalent bonding based process is generally strong and reliable, although simple dropping and incubating may also suffice
98	Damage to cells in resin excess removal (Supplementary Fig. 5)	Placing the sample vertically for too long or washing the sample with too much ethanol can cause detachment of cells and cracks of cellular structures (SI	The optimal resin removal depends on the area of the sample. Before wash the critical samples, test dummy samples of an area comparable to experimental samples
109	Charging in SEM imaging (Supplementary Fig. 6).	The sample is not conductive enough or well grounded	Properly ground the sample to the sample holder by connecting them with a conductive paste. We suggest to deposit approximately 10 nm of metal on to the specimen. This thickness can be adjusted depending on the sample composition (non-conductive polymer based samples might need 20–25 nm thick metal)
118	Curtaining effect (i.e., increased surface roughness in the direction of the milling depth) in polishing a cross section (Supplementary Fig. 8)	Underdose of the ion beam	Use low polishing currents (i.e. 80 pA) at a voltage of 30 kV