Rigorous finite-difference time-domain electromagnetic simulation is used to simulate the scattering from proto-typical pupil mask cross-section geometries and to quantify the differences from the normally assumed ideal on-off behavior. Shaped pupil plane masks are a promising technology for the TPF coronagraph mission. However the stringent requirements placed on the optics require that the detailed behavior of the edge-effects of these masks be examined carefully. End-to-end optical system simulation is essential and an important aspect is the polarization and cross-section dependent edge-effects which are the subject of this paper. Pupil plane masks are similar in many respects to photomasks used in the integrated circuit industry. Simulation capabilities such as the FDTD simulator, TEMPEST, developed for analyzing polarization and intensity imbalance effects in nonplanar phase-shifting photomasks, offer a leg-up in analyzing coronagraph masks. However, the accuracy in magnitude and phase required for modeling a chronograph system is extremely demanding and previously inconsequential errors may be of the same order of magnitude as the physical phenomena under study. In this paper, effects of thick masks, finite conductivity metals, and various cross-section geometries on the transmission of pupil-plane masks are illustrated. Undercutting the edge shape of Cr masks improves the effective opening width to within λ/5 of the actual opening but TE and TM polarizations require opposite compensations. The deviation from ideal is examined at the reference plane of the mask opening. Numerical errors in TEMPEST, such as numerical dispersion, perfectly matched layer reflections, and source haze are also discussed along with techniques for mitigating their impacts.