We have developed an improved vapor-phase deposition method and apparatus for the application of layers and coatings on various substrates. The method and apparatus are useful in the fabrication of biofunctional devices, Bio-MEMS devices, and in the fabrication of microfluidic devices for biological applications. In one important embodiment, a siloxane substrate surface is treated using a combination of ozone and UV radiation to render the siloxane surface more hydrophilic, and subsequently a functional coating is applied in-situ over the treated surface of the siloxane substrate.