Two-dimensional arrays of embedded channels with cross-sectional diameters of 1-3 m were fabricated in silica-on-silicon thin film structures. The channel arrays were fabricated using void-forming borophosphosilcate glass (BPSG) deposited by plasma-enhanced chemical vapor deposition (PECVD) over templates patterned and etched using standard photolithographic methods and reactive ion etching. The size and shape of the channels could be controlled by adjusting the depth, width, and spacing of the template ridges, the dopant levels in the BPSG, and the annealing conditions. Optimization of the channel fabrication process through detailed investigation of the process variables is presented. Potential applications in photonics, sensors, and microfluidics are discussed.