Ion milling has been used to transfer the nanometer scale, periodic pattern of a protein crystal ("S-layer") into the supporting substrate. At the same time, etch pits, attributable to the presence of surface contamination, evolve in random areas of the substrate not covered by the S-layer ("off-S-layer"). Using the theory of ripple topography proposed by Bradley and Harper, a computer simulation of hole formation based on curvature dependent sputtering and surface self-diffusion has been formulated. To determine the validity of this model as applied to the patterning process, profiles of actual etch pits have been obtained using atomic force microscopy, and the simulation has been used to evolve these profiles in time. Even with a number of simplifying assumptions in place, the model simulates the experimental data quite well.