Permineralization provides the most faithful known mode of three-dimensional preservation of the morphology and cellular anatomy of fossil plants. Standard optical microscopic documentation of such structures can provide only an approximation of their true three-dimensional form and is incapable of revealing fine-structural details, deficiencies that can be addressed by the use of confocal laser scanning microscopy (CLSM). To demonstrate the usefulness of CLSM, we compare confocal laser scanning micrographs and optical photomicrographs of the permineralized tissues of rhizomes and petioles of the Eocene fern Dennstaedtiopsis aerenchymata, preserved in cherts of the Clarno Formation of Oregon, USA, and the Allenby Formation (Princeton chert) of British Columbia, Canada. Characterization of fern morphology and anatomy with CLSM provides accurate data in two and three dimensions at high spatial resolution, information that can be critically important to taxonomic, taphonomic and developmental interpretations. Results presented here indicate that this non-intrusive, non-destructive technique should be widely applicable in paleobotany.