The Miniature Radio Frequency instrument (Mini-RF) on the Lunar Reconnaissance Orbiter obtained widespread synthetic aperture radar observations of the Moon in the S band (12.6 cm), including nearly complete coverage at both lunar poles. The currently archived monostatic data have spatial offsets from the lunar reference frame, making them more difficult to compare to other data sets. To address this issue, we have developed a new algorithm for spatially controlling the Mini-RF S-band monostatic data set and orthorectifying these data onto lunar topography. Additionally, as the influence of incidence angle changes on radar observations is well known, we describe an empirical approach to account for variations in observation geometry and surface topography. Individual radar swaths and mosaics produced using this method more clearly show the variability in scattering behavior due to changes in lunar regolith properties and suppress some of the behavior arising from these topographic effects alone. Once these terrain effects are taken into account, we find that areas of permanent shadow at both poles have a higher median radar reflectivity than nonpermanently shadowed regions, but the polarization behavior of shadowed versus unshadowed areas is largely similar. The higher radar reflectivity in permanent shadow is likely the result of physical or compositional differences in these unique environments, though the precise cause remains uncertain. The results here illustrate how reducing the influence of topography and geometry effects in Mini-RF radar data may enable better characterization of lunar geologic units, regolith structure, and potential areas hosting volatile deposits at the lunar poles.