Broad ion beam (BIB) milling is useful in organic petrology because it can yield flat sample surfaces and avert the 'smearing' of organic matter (OM) that results from traditional mechanical polishing. This potentially makes BIB especially useful in the study of nano-porosity, where even minor mechanical disruption of the sample surface distorts the sample characteristic of interest the pore structure. However, several studies have observed an OM reflectance increase after BIB milling, concluding that ion milling may cause thermal alteration to OM surfaces. To better understand ion milling effects on organic matter, coal (subbituminous, high volatile bituminous, medium volatile bituminous, anthracite) and shale [Bakken Formation, Ohio Shale-Huron Member (5), Kimmeridge Clay Formation, Alum Shale, New Albany Shale] samples were prepared using traditional mechanical polishing methods. Reflectance measurements (% R-o) were gathered on all maceral types present before BIB milling, followed by re-measurement of OM reflectance at the same locations after milling. Most OM increased in reflectance after BIB milling, with some exceptions in high maturity samples. Liptinite macerals in both coal and shale samples showed the greatest percent reflectance increase on average (+ 133%; n = 338), followed by solid bitumen (+ 49%; n = 313), vitrinite (+ 26%; n = 413), and inertinite (+ 9%; n = 220). Despite the increases to OM reflectance caused by BIB milling, no evidence was found for kerogen conversion (e.g., change in maceral abundances), or for migration of newly generated petroleum (e.g., pseudomorphic replacement of kerogen by solid bitumen). Such changes occur when samples are thermally altered from immature conditions into the oil window (e.g., by hydrous pyrolysis), and, if the increases in OM reflectance were thermally driven (by BIB milling), they should have been observed in the above experiments. Herein, we also used atomic force microscopy to document a decrease in surface roughness of correlative locations of OM on pre- and post-ion milled samples. This improved surface polish caused by BIB milling appears to be the root cause of increased OM reflectance, as no other supporting evidence of thermal alteration could be found. That is, the fraction of light formerly lost to oblique scatter in diffuse reflectance from a mechanically polished surface is converted to specular reflectance after BIB ion milling. Thus the light leaves the surface at a near normal angle and returns to the detector, resulting in increased OM reflectance.