A Direct Simulation Monte Carlo (DSMC) method is utilized to simulate gas diffusion in nanoscaled highly porous layers. An open source solver has been extended with the variable soft sphere (VSS) binary collision model and the inflow boundary model was adjusted for small numbers of DSMC particle initialization. Comparison with the analytical diffusion equation illustrate the improvement of the VSS model compared to the variable hard sphere model (VHS). Subsequently, several highly porous particle layers (gas sensors synthesized by flame spray pyrolysis and isotropic layers) build up by 10 nm particles have been investigated. Results for DSMC gas diffusion in the porous structures are in agreement with the well established dusty gas model (DGM). However, while DGM requires measurements or estimations of pore sizes, porosity, and tortuosity and furthermore is limited to homogenous layers, the present contribution shows significant advantages of DSMC in describing gas diffusion in non-isotropic porous structures.