Gas/wall collision mechanisms play a key role in Knudsen diffusion process. In particular, the channel wall structure has a major influence in mass transfer. So, we investigate the influence of the wall roughness, anisotropy and porosity on the self-diffusion of helium and neon in nanochannels. Three materials are proposed: graphite and β-cristobalite and amorphous silica. The study makes it possible to analyze, in function of temperature, the correlation between 1/the ballistic/diffusion transition regime of the surface gas transfer, 2/the transition of the bouncing process to a linear increase of the bounce number with time and 3/the shape of the surface residence time distribution characterized by a Fréchet like distribution at short time and an exponential decay at long time. As concerns the amorphous SiO 2 , the bounce must be redefined owing to the transfer inside the material which is dominated by a cage effect. The anisotropy effect on collision process and Knudsen diffusion is analyzed by means of a tensorial computation of the tangential momentum accommodation coefficient and of the mean square displacement. Using the Langevin at the channel scale and the Arya model, the ballistic/diffusion transition time of the mean square displacement is related to the collision frequency and the collision number required for the velocity to be uncorrelated. A stochastic model confirms the molecular dynamics results with β-SiO 2 channel: The behavior of the Knudsen diffusion coefficient according to the Arrhenius law and the influence of collision frequency on transition time.