Systems and techniques are described for topography simulation of etching and/or deposition on a physical structure. The structural information can be represented using a three-dimensional (3D) voxel grid data structure. For each particle emitted by a Monte-Carlo particle emission model, a topographical modification caused by the particle can be determined by (1) calculating fluxes, (2) evaluating surface reactions, and (3) modifying the physical structure. The effect of the etching and/or deposition on a physical structure can be displayed by rendering the 3D voxel grid data structure.