The skin surface structure of squamate reptiles varies greatly among species, likely because it plays a key role in a range of tasks, such as camouflage, locomotion, self‐cleaning, mitigation of water loss and protection from physical damage. Although we have foundational knowledge about squamate skin morphology, we still know remarkably little about how intraspecific variation in skin surface structure translates to functional variation. This gap in our understanding can be in part traced back to: (i) our lack of knowledge on how body size determines skin surface structure; and (ii) the lack of means to perform high‐throughput and detailed analysis of the three‐dimensional (3D) anatomy of reptilian skin surfaces in a non‐destructive manner. To fill this gap, we explored the possibilities of a new imaging technique, termed gel‐based stereo‐profilometry, to visualize and quantify the 3D topography of reptilian skin surface structure. Using this novel approach, we investigated intra‐specific and intra‐individual variation in the skin surface morphology of a focal lizard species, Anolis cristatellus. We assessed how various characteristics of surface topography (roughness, skew and kurtosis) and scale morphology (area, height, width and shape) scale with body size across different body regions. Based on an ontogenetic series of A. cristatellus males, we show that skin roughness increases with body size. Skin patches on the ventral body region of lizards were rougher than on the dorsum, but this was a consequence of ventral scales being larger than dorsal scales. Dorsal surface skew and kurtosis varied with body size, but surfaces on the ventral skin showed no such relationship. Scale size scaled isometrically with body size, and while ventral scales differed in shape from dorsal scales, scale shape did not change with ontogeny. Overall, this study demonstrates that gel‐based stereo‐profilometry is a promising method to rapidly assess the 3D surface structure of reptilian skin at the microscopic level. Additionally, our findings of the explanatory power of body size on skin surface diversity provide a foundation for future studies to disentangle the relationships among morphological, functional and ecological diversity in squamate reptile skin surfaces.