Ion milling is increasingly used as a mean of sample surface preparation for scanning electron microscopy (SEM) to provide high-resolution imagery needed for studying the nanoscale structure of mudstones. Application of this technique has introduced new insight into nano-structural properties within organic matter (i.e., organic porosity) as an important reservoir control factor in unconventional shale/tight rocks. The continuous bombardment of the sample surface by ions (e.g., Gallium, Argon) results in the formation of kinetic heat energy, hence heating the milled surface of the rock. While this technique has proven to provide a spectacular surface for studying the fine structures, the effect of initial heat transfer to the organic matter (OM) is not well understood. Optical properties of OM (reflectance and fluorescence spectrometry) respond to the degree of aromatization of organic molecules, caused by thermal alteration. The effects of ion milling on dispersed OM were studied on four different macerals (i.e., solid bitumen, pyrobitumen, zooclasts, and alginate) within mudrocks of different thermal maturity levels. These mudrocks were milled with a cryogenic broad ion beam (C-BIB) and a focused ion beam (FIB). The random reflectance (Ro), bi-reflectance and the fluorescence red/green quotient (Q) of the macerals were measured and compared before and after the milling processes. The results show that initial heating caused by ion bombardment results in significant thermal alteration of the OM surfaces. The C-BIB milling resulted in 10 to 53% increase in the Ro values of the studied macerals, depending on their initial chemical refractoriness. The higher energy FIB milling increased Ro values of the same macerals by one order of magnitude. The solid bitumen appears to be more susceptible to thermal alteration than more refractory macerals (e.g., zooclasts and pyrobitumen). Ion milling did not shift the fluorescence spectra in immature alginate, suggesting that thermal alteration caused by ion milling is limited to the surface and not the entire body of the maceral. This study also documents significant morphological and possible chemical changes in pyrite due to the ion beam incident thermal alteration in most samples. Since most ion beam SEM studies focus on organic nanoporosity within the OM, thermal alteration caused by ion milling may have serious implications for image-based physical analysis of pores. The possibility of increased nanoporosity due to rapid devolatilization of lighter organic compounds in macerals could potentially have a significant impact on organic porosity, especially at lower thermal maturities (i.e., oil and wet gas windows). Crown Copyright (C) 2016 Published by Elsevier B.V. All rights reserved.