A significant number of oil paintings produced by Georgia O’Keeffe (1887–1986) show surface protrusions of varying width, up to several hundreds of microns. These protrusions are similar to those described in the art conservation literature as metallic soaps. Since the presence of these protrusions raises questions about the state of conservation and long-term prospects for deterioration of these artworks, a 3D-imaging technique, photometric stereo using ultraviolet illumination, was developed for the long-term monitoring of the surface shape of the protrusions and the surrounding paint. Because the UV fluorescence response of painting materials is isotropic, errors typically caused by non-Lambertian (anisotropic) specularities when using visible reflected light can be avoided providing a more accurate estimation of shape. As an added benefit, fluorescence provides additional contrast information contributing to material characterization. The developed methodology aims to detect, characterize, and quantify the distribution of micro-protrusions and their development over the surface of entire artworks. Combined with a set of analytical in situ techniques, and computational tools, this approach constitutes a novel methodology to investigate the selective distribution of protrusions in correlation with the composition of painting materials at the macroscale. While focused on O’Keeffe’s paintings as a case study, we expect the proposed approach to have broader significance by providing a non-invasive protocol to the conservation community to probe topological changes for any relatively flat painted surface of an artwork, and more specifically to monitor the dynamic formation of protrusions, in relation to paint composition and modifications of environmental conditions, loans, exhibitions, and storage over the long term.