Research examining organic-matter hosted porosity has significantly increased during the last ten years due to greater focus on understanding hydrocarbon migration and storage in source-rock reservoirs, and technological advances in scanning electron microscopy (SEM) capabilities. The examination of nanometer-scale organic-matter hosted porosity by SEM requires the preparation of exceptionally flat geologic samples beyond the abilities of traditional mechanical polishing which can deform or otherwise obscure organic surfaces. To meet this demand, broad ion beam (BIB) milling was introduced as a sample preparation technique for SEM petrographic analysis of geologic samples. But like with any sample preparation technique, there can be unintended consequences. In this study, we examined the development of nanometer-scale pore-like features caused by BIB milling of thermoset plastic binder material [poly(methyl methacrylate), PMMA] used for the mounting of geologic samples, and artifact pore-like features in the organic matter of Eocene Mahogany zone of the Green River Formation and Jurassic Kimmeridge Clay Formation source rocks.