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A vapor phase deposition system was designed to coat uniform, conformal and ultrathin coatings of fluoropolymer and fluorosilane thin films inside silicon nanochannels. Surface modifications using vapor phase deposition become increasingly important for biomedical micro/nanoelectromechanical system (BioMEMS/NEMS) applications and have advantages over liquid phase deposition since the vapor can permeate more efficiently into silicon nanochannels. In this article, we explore the use of vapor phase deposition to deposit ultrathin films of two fluoropolymers and a fluorosilane, identifying deposition parameters to optimize the process. The films are desirable to control the hydrophobicity of the surface and reduce or prevent undesired protein adsorption or cell interactions, which may cause detrimental effects to the performance of most BioMEMS/NEMS devices. The films were characterized by means of a contact angle analyzer for hydrophobicity and an ellipsometer for film thickness. Atomic force microscopy was used extensively to collect surface images, adhesive and frictional properties of these films, all of which play a very important role in characterizing uniform, conformal and ultrathin films on the surface.