The selective deposition of GaAs and InP was investigated using a multiscale approach. Local gas phase composition, temperature, and flow fields were calculated solving mass, energy and momentum conservation equations at the reactor scale with 2D FEM. The growth on patterned wafers was described with a 2D microscale model that includes adsorption and diffusion on mask and feature. Reactor and microscopic models are linked consistently imposing the continuity of gas phase fluxes. The morphology evolution was investigated with 3D KMC using gas phase fluxes calculated with the microscopic scale model. The model is generally in good agreement with experimental data except for high mask/feature ratios, in which case the growth rate is overestimated both for GaAs and InP. We attribute the overestimation to the diffusion of molecular species adsorbed on (1 1 1) facets from feature to mask. (C) 2004 Elsevier B.V. All rights reserved.