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Microstructural properties of thin-film absorber layers play a vital role in developing high-performance solar cells. Scanning probe microscopy is frequently used for measuring spatially inhomogeneous properties of thin-film solar cells. While powerful, the nanoscale probe can be sensitive to the roughness of samples, introducing convoluted signals and unintended artifacts into the measurement. Here, we apply a glancing-angle focused ion beam (FIB) technique to reduce the surface roughness of CdTe while preserving the subsurface optoelectronic properties of the solar cells. We compare the nanoscale optoelectronic properties “before” and “after” the FIB polishing. Simultaneously collected Kelvin-probe force microscopy (KPFM) and atomic force microscopy (AFM) images show that the contact potential difference (CPD) of CdTe pristine (peak-to-valley roughness > 600 nm) follows the topography. In contrast, the CPD map of polished CdTe (< 20 nm) is independent of the surface roughness. We demonstrate the smooth CdTe surface also enables high-resolution photoluminescence (PL) imaging at a resolution much smaller than individual grains (< 1 μm). Our finite-difference time-domain (FDTD) simulations illustrate how the local light excitation interacts with CdTe surfaces. Our work supports low-angle FIB polishing can be beneficial in studying buried sub-microstructural properties of thin-film solar cells with care for possible ion-beam damage near the surface.