Mesoscale polymer ribbon arrays are high aspect ratio surface structures that exhibit unique three-dimensional morphologies in aqueous environments. To better correlate the impact of processing and aging on the morphology of these and similar high-aspect ratio surface structures, we have developed a MATLAB code capable of extracting quantitative morphological descriptors from 3D confocal microscopy data. This code was used to produce the results outlined in “Mesoscale Polymer Arrays: High Aspect Ratio Surface Structures and Their Digital Reconstruction.” In addition to this code, we have included instructions for data processing and four test datasets. This process first skeletonizes .tif stacks obtained via confocal microscopy. It then builds a model of individual ribbon positions in 3D space. Finally, it calculates key quantitative morphological descriptors such as the radius of curvature and end-to-end distance of these high aspect ratio structures.