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 biotechnologically functional devices, Bio-MEMS devices, and in the fabrication of microfluidic devices for biological applications. In one important embodiment, oxide coatings providing hydrophilicity or oxide/polyethylene glycol coatings providing hydrophilicity can be deposited by the present method, over the interior surfaces of small wells in a plastic micro-plate in order to increase the hydrophilicity of these wells. Filling these channels with a precise amount of liquid consistently can be very difficult. This prevents a water-based sample from beading up and creating bubbles, so that well can fill accurately and completely, and alleviates spillage into other wells which causes contamination.