The present invention relates to a process for fabricating microchannels on a substrate and to a substrate comprising these microchannels, the invention being especially applicable to the fabrication of microstructured substrates for microelectronic, microfluidic and/or micromechanical systems.The process includes a step (a) of producing at least one or at least two patterns 2 on the surface of a bottom layer 1 and a step (b) of depositing, on top of the bottom layer and the pattern or patterns, a layer 3 of polymer material obtained by polymerizing an organic or organometallic monomer that contains siloxane functional groups, for example tetramethyldisiloxane, in a plasma-enhanced, optionally remote plasma-enhanced, chemical vapor deposition reactor (PECVD or optionally RPECVD) reactor.The layer of polymer material is deposited so as to create, in place of the pattern and after development by decomposing this pattern, or between the two patterns without development/decomposition, a channel 4a, 4b, 4c, 4d closed over at least part of its length.