Paleontologists routinely study fossils using high-magnification and high-resolution backscattered electron (BSE) images acquired via scanning electron microscopy (SEM). In BSE imaging, contrast corresponds to differences in backscattering of primary electrons and BSE detection among points in the electron beam raster scan. In general, BSE images are known for compositional contrast corresponding to backscattering monotonically related to average atomic number. However, two other types of contrast are relevant to BSE-SEM of fossils: (1) topographic contrast corresponding to backscattering and BSE detection varying with specimen shape and (2) mass-thickness contrast corresponding to backscattering varying with the relative masses and thicknesses of materials in the uppermost few microns of a sample. Here, we demonstrate the significance of these contrast mechanisms for resolving three-dimensional and subsurficial features of fossils. First, we show—through study of mass-thickness contrast in BSE images of carbonaceous compressions from the Triassic Solite Quarry Lagerstätte (Virginia)—that some tissues (e.g., leaf and insect wing veins) are preserved as thicker carbonaceous films than others (e.g., leaf laminae and insect wing membranes), possibly reflecting taphonomic differences among anatomical tissues. Second, we show that the problematic phosphatic shelly fossil Sphenothallus (lower Cambrian, China) is covered by low-relief transverse ribs and made up of exteriorly sculptured and interiorly unsculptured carbon- and phosphorus-rich layers with microstructures. Taking advantage of both topographic and mass-thickness contrast mechanisms, these case studies demonstrate that BSE imaging elucidates morphological details that are not obvious in surficial light microscopy or secondary-electron SEM and are otherwise only evident via tomography.