SU-8 is a negative-tone photoresist that can serve as a complete optical bench for micro-photonic systems. Functional optical devices and passive alignment structures can all be formed in the same material system with common processing steps. Many interrelated process parameters control the final geometry of structures formed in SU-8, but all can be accurately simulated and predicted by computer modeling. In this work, a comprehensive model of the lithography process was developed and combined with rigorous electromagnetic simulation. It was applied to predict sidewall slope of a tall structures as well as the geometry and transmission spectra of a three-dimensional photonic crystal. The model is seen as an enabling step toward realizing optimized micro-photonic systems in SU-8.