To test if reflectance increases to sedimentary organic matter (vitrinite) caused by broad ion beam (BIB) milling were related to molecular aromatization and condensation, we used Raman and Fourier transform infrared (FTIR) spectroscopies 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 expressed by the areal root-mean-square roughness parameter Rq). Samples consisted of four medium volatile bituminous coals. We used a non-aggressive BIB milling approach 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 (VRo) increases of 12 to 36 percent of the original values. When molecular proxies from FTIR (e.g., A- and C-factor, branching ratio) were plotted against each other for the same vitrinite locations pre- and post-milling, data points generally lie within error of a 1:1 line. Likewise, Raman thermal proxy (e.g., G-FWHM, RBS and D1/G) 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 after BIB milling. We interpret these results to indicate VRo increase induced by gentle BIB milling is an effect of decreased diffuse reflectance due to flatter surfaces, causing more photons to reflect directly back to the detector. We see little evidence for molecular aromatization and condensation of vitrinite molecules following BIB milling with the conditions used in our study. Observed 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.