Physical deposition processes for thin film optical coatings are modeled in the Virtual Coater framework. This concept combines different simulation techniques in a multi scale model, which covers the material transport in the coating plant, the atomistic growth of the thin films and electronic and optical properties of these films. The material transport is simulated by Direct Simulation Monte Carlo and the atomistic growth is performed by classical molecular dynamics. For the calculation of optical properties usually the density functional theory can be employed, but only for a limited structural size in the order of about 100 atoms. The structural properties, that cannot be described by this limited number of atoms, like voids and pores, therefore needs to be described by effective medium approximations, for example. This approach allows to describe the impact of structural inhomogeneities on the optical properties. Pores amount and orientation can be modeled to obtain direction dependent effective index ellipsoids. However, for applying the effective medium theory, the optical properties of the different dense materials need to be known, which can be obtained by the density functional theory. The possibilities and limitations of the approach are discussed.