In this article, the fabrication process of annular photonic crystals on silicon-on-insulator wafers was addressed for the first time. A self-alignment procedure for nanofabrication using atomic layer deposition and sacrificial etching was established to place accurately nanosized dielectric rods in nanosized circular air holes. Avoiding the challenging electron-beam lithography alignment, this method achieves atomic level precision and shows high stability. (C) 2009 American Vacuum Society. [DO]: 10.1116/1.3079662]