The plant epidermis regulates key physiological functions contributing to photosynthetic rate, plant productivity, and ecosystem stability. Yet, quantitative characterization of this interface between a plant and its aerial environment is laborious and destructive with current techniques, making large-scale characterization of epidermal cell parameters impractical. Here, we present our exploration of optical topometry (OT) for the analysis of plant organ surfaces. OT is a mature, confocal microscopybased implementation of surface metrology that generates nanometer-scale digital characterizations of any surface. We report epidermal analyses in Arabidopsis (Arabidopsis thaliana) and other species as well as dried herbarium specimens and fossilized plants. We evaluate the technology's analytical potential for identifying an array of epidermal characters, including cell type distributions, variation in cell morphology and stomatal depth, differentiation of herbarium specimens, and real-time deformations in living tissue following detachment. As applied to plant material, OT is very fast and nondestructive, yielding richly mineable data sets describing living tissues and rendering a variety of their characteristics accessible for statistical, quantitative genetic, and structural analysis.High-throughput methodologies are enabling ever more precise and integrated analyses of plant genomes, transcriptomes, proteomes, and metabolomes. However, connecting such comprehensive molecular data sets to the higher orders of plant organization that they control depends upon capturing correspondingly precise and authentic quantitative depictions of plant cell biology, anatomy, and developmental features. Highthroughput phenotyping techniques, enabling the speed and accuracy of data acquisition characteristic of omic technologies, are now needed if we are to forge mechanistic links between macroscopic plant phenotypes and their molecular underpinnings.This report addresses the challenge of structurally phenotyping the plant epidermis. A widely used and cost-effective method for quantifying epidermal phenotypes employs nail polish and/or dental resin to create an impression of the tissue surface, followed by imaging under light microscopy (Geisler et al., 2000;Delgado et al., 2011). Resultant images are then manually quantified using image analysis software such as ImageJ or Cell Profiler, yielding outputs such as cell sizes, stomatal index (number of stomata per total cell number), or stomatal density (number of stomata per unit area). Methods appropriate for smaller scale studies involve tissue fixation and staining or transgenic marker lines (Dow et al., 2014;Lawson et al., 2014). These current methods share common disadvantages of tedious sample preparation and low throughput. More elaborate methods involving fluorescence and electron microscopy are encumbered by the additional disadvantage of higher imaging equipment costs (Salomon et al., 2010). Finally, nearly all of these methods are somewhat or completely destructive, allo...