Monte Carlo simulation is deemed to be the leading algorithm for accurate dose calculation with electron beams. Patient anatomy (contours and tissue densities) as well as irradiation geometry is accounted for. The accuracy of the Monitor Unit (MU) determination is one essential aspect of a treatment planning system. Patient-specific quality assurance of a Monte Carlo plan usually involves verification of the MUs with an independent simpler calculation approach, in which flat geometry is to be assumed. The magnitude of the discrepancies between flat and varied surfaces for a few scenarios has been investigated in this study. The ability to predict MUs for various surface topologies by the commercial electron Monte Carlo implementation from Varian Eclipse system (Eclipse eMC) has been evaluated and compared to the Generalized Gaussian Pencil Beam (GGPB) algorithm. Ten phantoms with different topologies were constructed of water-equivalent material. Measurements with a parallel plate ionization chamber were performed using these phantoms to gauge their relative impact on outputs for 6, 9, 12, 16, and 20MeV electron beams from a Varian TrueBeam with cone sizes ranging from 6 × 6 cm2 to 25 × 25 cm2. The corresponding Monte Carlo simulations of the measured geometries were carried out using the CT scans of these phantoms. The results indicated that the Eclipse eMC algorithm can predict these output changes within 3% for most scenarios. However, at the lowest energy, the discrepancy was the greatest, up to 6%. In comparison, the Eclipse GGPB algorithm had much worse agreement, with discrepancies up to 17% at the lowest energies.