For the study of the Pleistocene reef microbialites from Hawaii, samples were examined under a scanning electron microscope (SEM) to identify microbial features allowing for biological identification. With SEM imaging of microbialite surfaces and vertical polished sections, we characterize the ultrastructure of the crusts and identify trapped and bound particles as well as any microbial remains that might allow identification of the microbes, e.g., filaments that are indicative of taxonomic determination. SEM analysis with a secondary electron (SE) detector was performed with a Teneo-VS SEM at the KAUST Imaging and Characterization Core Lab, and a Tescan Vega LMU at the ZMT Geosciences Laboratory.