The direct simulation Monte Carlo (DSMC) technique was used to model the flow around multiple features on a wafer. Since the DSMC technique is valid in both the continuum and rarefied flow regimes, the near-surface reactor flow was directly coupled with the features into a single reactor-feature scale model. This model was then used to determine the effects of operating conditions, feature geometry, and surface chemistry on the concentrations and fluxes to a hat and featured surface. The surface chemistry addressed both chlorine etching of aluminum and SiO2 deposition from a silane/oxygen/argon gas mixture. For both the etch and deposition cases, the concentration of products was higher near the featured surface than the flat surface. This was partially due to multiple molecular reflections between the horizontal and vertical surfaces of the features. While the reacting area of the features was greater than the flat surface with no features, the fluxes to the features were less due to the direction of the incoming flow. Thus, topography models using fluxes to flat surfaces, which are assumed in full reactor scale models, will overpredict deposition or etch rates. A simplified adjustment to the flat surface flux was made to obtain more accurate boundary conditions for topography models and thus, better predictions of deposition and etch rates.