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Parylene C is a biocompatible polymer that has been investigated as an encapsulation material for implantable microsystems. Since parylene C is deposited directly on the substrate from the vapor phase it can conform to a wide range of geometries. However, the thickness of the deposited layer tends to decrease in microscale gaps, which might lead to an insulation failure. To ensure more robustness of the coating, the changes in parylene C coating thickness have been investigated experimentally using simple gaps of known dimensions. In an attempt to better understand these experimental findings, two theoretical models have been developed. The first one, which is based on a diffusion approximation, is able to reproduce and extrapolate the experimental results, leading to a useful design rule for practical applications involving parylene C coating. As an example, we present the substrate design of a flexible sieve electrode for a peripheral nerve interface. The second model aims at an appropriate microscopic description of the coating process in terms of kinetic theory of gases.