The main focus of this work is put on three-dimensional simulations of a topography changing process, especially for the simulation of thin film deposition and etching with particle transport in rarefied gas phases. This chapter attempts to integrate a wide range of popular models within a generalized version of the ballistic transport and reaction model (BTRM) [21]. In the following section, physical models for the description of the solid body, the particle transport to the surface, as well as the surface reaction are discussed.