In this paper we combine a stochastic 3D microstructure model of a fiber based gas diffusion layer of polymer electrolyte fuel cells with a Lattice Boltzmann model for fluid transport. We focus on a simple approach of compressing the planar oriented virtual geometry of paper-type gas diffusion layer from Toray. Material parameters -permeability and tortuosity -are calculated from simulation of one phase, one component gas flow in stochastic geometries. We analyze the statistical spread of simulation results on ensembles of the virtual geometry, both uncompressed and compressed. The influence of the compression is discussed with regard to the Kozeny-Carman equation. The effective transport properties calculated from transport simulations in compressed gas diffusion layers agree well with a trend based on the Kozeny-Carman equation.