A process for forming one or more fluid microchannels on a substrate is disclosed that is compatible with the formation of integrated circuitry on the substrate. The microchannels can be formed below an upper surface of the substrate, above the upper surface, or both. The microchannels are formed by depositing a covering layer of silicon oxynitride over a mold formed of a sacrificial material such as photoresist which can later be removed. The silicon oxynitride is deposited at a low temperature (.ltoreq.100.degree. C.) and preferably near room temperature using a high-density plasma (e.g. an electron-cyclotron resonance plasma or an inductively-coupled plasma). In some embodiments of the present invention, the microchannels can be completely lined with silicon oxynitride to present a uniform material composition to a fluid therein. The present invention has applications for forming microchannels for use in chromatography and electrophoresis. Additionally, the microchannels can be used for electrokinetic pumping, or for localized or global substrate cooling.