In this article, we present a simulation tool for modeling a quasi-optical bench for material characterization. The model uses a Gaussian beam expansion and tracking analysis, together with a modal analysis to enable a comparison of the simulated reflection and transmission S-parameters to the ones measured with a 4-port vector network analyzer. A Thru-Reflect-Line calibration is performed to de-embed the simulated S-parameters of a dielectric slab located between two lens antennas, showing good agreement with the analytical slab model used for experimental permittivity extraction.