Based on the autocloning technique the photonic crystals were fabricated using E-beam gun evaporation with ion-assisted deposition (IAD) on the periodic corrugation patterns of substrates. In this research, the surface evolution function based on the unified process model was simulated to analyze the influence of the etching and redeposition effects of the different etching time. As the etching time was longer, the top roof angle was larger and the redeposition thickness was getting thicker. The difference of the top roof angle in the experiment and the simulated result are less than 4A degrees. It shows the simulation method achieved very good agreement with the fabricated result for different etching times from 40 to 120 min. We found the surface angular was depended on the etching effect more than the redeposition effect.