Numerical simulation of gas molecules scattering by the rough surface and estimation of surface structure influence on free molecular gas flow in cylindrical micro channels have been carried out. The surface structure is reconstructed according to Atomic Force Microscopy data obtained for Si-based samples with the use of developed procedure. The dependence of monochromatic molecular beam scattering on incident angle has been investigated. The developed technique gives analytical form of velocity distribution function for particles reflected from the rough surface. The calculation of gas flow in terms of channel's molecular conductivity is based on Monte-Carlo test particle method.