The ongoing miniaturization in electronics poses various challenges in the designing of modern devices and also in the development and optimization of the corresponding fabrication processes. Computer simulations offer a cost- and time-saving possibility to investigate and optimize these fabrication processes. However, modern device designs require complex three-dimensional shapes, which significantly increases the computational complexity. For instance, in high-resolution topography simulations of etching and deposition, the evaluation of the particle flux on the substrate surface has to be re-evaluated in each timestep. This re-evaluation dominates the overall runtime of a simulation. To overcome this bottleneck, we introduce a method to enhance the performance of the re-evaluation step by calculating the particle flux only on a subset of the surface elements. This subset is selected using an advanced multi-material iterative partitioning scheme, taking local flux differences as well as geometrical variations into account. We show the applicability of our approach using an etching simulation of a dielectric layer embedded in a multi-material stack. We obtain speedups ranging from 1.8 to 8.0, with surface deviations being below two grid cells (0.6–3% of the size of the etched feature) for all tested configurations, both underlining the feasibility of our approach.