A major difficulty that has long hindered studies of organic-walled Precambrian microbes in petrographic thin sections is the accurate documentation of their three-dimensional morphology. To address this need, we here demonstrate the use of confocal laser scanning microscopy. This technique, both non-intrusive and non-destructive, can provide data by which to objectively characterize, in situ and at submicron-scale resolution, the cellular and organismal morphology of permineralized (petrified) microorganisms. Application of this technique can provide information in three dimensions about the morphology, taphonomy, and fidelity of preservation of such fossils at a spatial resolution unavailable by any other means.