Over the last two decades, considerable research has been devoted to micro-optic and now nano-optical structures. Fabrication methods have become sufficiently mature to realize most concepts, but due to physics inherent in the process, geometry is distorted. Edges are rounded, sidewalls are sloped, surfaces are rough, and etching or deposition not uniform. Deviations from "perfect" geometry can dramatically affect optical behavior. In order to address the impact of the "non-perfect" nature of fabrication, numerical methods for modeling fabrication is discussed and quantified for various examples. As an example, comprehensive modeling of near-field nano-patterning is described. Numerical and experimental results are presented of three-dimensional photonic crystals fabricated in a contact mask aligner using a standard UV lamp as the source.© (2006) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.