Ultrathin coatings of fluorosilane films for silicon and polydimethylsiloxane (PDMS) nanochannels are desirable to control the hydrophobicity of the surface and reduce or prevent undesired protein adsorption or cell interactions critical for the performance of most biomedical micro/nanodevices. Surface modifications using vapor-phase deposition become increasingly important for some biomedical nanodevices and have advantages over liquid-phase deposition since the vapor phase can permeate more efficiently into silicon nanochannels. In this study, vapor-phase deposition was used to deposit ultrathin films of four fluorosilanes on silicon and PDMS and identify deposition conditions for an optimal process. The films were characterized by means of a contact angle analyser for hydrophobicity, an ellipsometer for film thickness, and an atomic force microscope for surface roughness of these films. Results of this study and relevant mechanisms are the subject of this article. (c) 2006 American Vacuum Society.