Ion milling applications in the micro-electronics industry are becoming more challenging due to decreasing feature sizes and increasing aspect ratios. A simulation of the milling problem which is capable of predicting surface evolution in the presence of high aspect ratios where local shadowing of the substrate surface becomes an important issue is described. A method of characteristics solution based on surface inclination angles is derived for a three-dimensional surface evolution model. An algorithm is developed to account for local shadowing effects, where raised areas of the substrate surface (i.e.. the photomask) prevent the ion beam from reaching hidden or shadowed portions of the surface. The yield (sputtering) function is modified to account for beam voltage as well as the angle of beam incidence. Yield function parameters are determined experimentally for Al2O3, Ti, permalloy (83/17 wt % Ni-Fe) and postbaked AZ P4400 photoresist. Model predictions are in good agreement with experimental results for the surface evolution of a photopatterned Al2O3 substrate.