Previous work has proposed transfer of kinetic heat energy from low-energy broad ion beam (BIB) milling causes thermal alteration of sedimentary organic matter, resulting in increases of organic matter reflectance. Whereas, other studies have suggested the organic matter reflectance increase from BIB milling is due to decreased surface roughness. To test if reflectance increases to sedimentary organic matter (vitrinite) caused by BIB milling were related to molecular aromatization and condensation, Raman and Fourier transform infrared (FTIR) spectroscopies were used to evaluate potential compositional changes in the same vitrinite locations pre- and post-BIB milling. The same locations also were examined by atomic force microscopy (AFM) to determine topographic changes caused by BIB milling (as quantified by the areal root-mean-square roughness parameter S_q). Samples consisted of four medium volatile bituminous coals. A non-aggressive BIB milling approach was used with conditions of 5 min, 4 keV, 15°incline, 360° rotation at 25 rpm and 100% focus (1.5 kV discharge; ∼100 μA). This gentle BIB milling caused vitrinite reflectance (VR_o) increases of 12 to 36% of the original values determined optically before milling (average 26% increase). When molecular proxies from FTIR (A- and C-factor, branching ratio) were plotted against each other for the same vitrinite locations pre- and post-milling, mean data points for each sample generally lie within error of a 1:1 line. Likewise, mean Raman thermal proxy [full-width half maximum of G-band (G-FWHM), Raman band separation (RBS) and D1/G band intensity ratio] values were similar for pre- and post-milled locations, also plotting within error of a 1:1 line. AFM confirms the majority (24 of 36) of pre- and post-ion milled surface pairs were smoother (lower S_q values) after BIB milling. These results are interpreted to indicate VR_o increase induced by the gentle BIB milling conditions used in this study is an effect of decreased diffuse reflectance due to flatter surfaces, causing more photons to reflect directly back to the detector. Little evidence was observed for molecular aromatization and condensation of vitrinite molecules following BIB milling (with the conditions used). The presence of milling-induced artifacts, including differential milling effects dependent on location and the development of self-organized patterned structures, indicate much work remains in standardization of BIB milling before its promulgation as a routine sample preparation technique for organic petrography. These results provide better understanding of anthropogenic-induced changes to geological samples caused by the now widespread adoption of BIB milling as a disruptive innovation in sample preparation.