We present a homogenization technique for rarefied gas flow over a microstructured surface consisting of patterns of periodic features. The length scale of the model domain is comparable to the mean free path of the molecules, while the scale of the surface patterns is much smaller. The flow is modeled by a system of linear Boltzmann equations with a diffusive boundary condition at the patterned surface. The resulting homogenized boundary condition holds at a virtual flat surface and incorporates the microscopic geometry information about the surface structure on the macroscopic level. Numerical results validate the approach. The setup models low pressure chemical vapor deposition processes in the manufacturing of integrated circuits.