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The application of micro- and nanofabrication processes to the development of hybrid synthetic and biological systems may enable the production of new devices such as controllable transporters, gears, levers, micropumps, or microgenerators powered by biological molecular motors. However, engineering these hybrid devices requires fabrication processes that are compatible with biological materials such as kinesin motor proteins and microtubules. In this paper, the effects of micro- and nanofabrication processing chemicals and resists on the functionality of casein, kinesin, and microtubule proteins are systematically examined to address the important missing link of the biocompatibility of micro- and nanofabrication processes needed to realize hybrid system fabrication. It is found that both casein, which is used to prevent motor denaturation on surfaces, and kinesin motors are surprisingly tolerant of most of the processing chemicals examined. Microtubules, however, are much more sensitive. Exposure to the processing chemicals leads to depolymerization, which is partially attributed to the pH of the solutions examined. When the chemicals were diluted in aqueous buffers, a subset of them no longer depolymerized microtubules and in their diluted forms still worked as resist removers. This approach broadens the application of micro- and nanofabrication processes to hybrid synthetic and biological system fabrication.