An epoxy-based negative-tone photoresist, which is known as a suitable material for high-aspect-ratio surface micromachining, is functionalized with red-light-emitting CdSe@ZnS nanocrystals (NCs). The proper selection of a common solvent for the NCs and the resist is found to be critical for the efficient incorporation of the NCs in the epoxy matrix. The NC-modified resist can be patterned by standard UV lithography down to micrometer-scale resolution, and high-aspect-ratio structures have been successfully fabricated on a 100 mm scaled wafer. The “as-fabricated”, 3D, epoxy-based surface microstructures show the characteristic luminescent properties of the embedded NCs, as verified by fluorescence microscopy. This issue demonstrates that the NC emission properties can be conveniently conveyed into the polymer matrix without deteriorating the lithographic performance of the latter. The dimensions, the resolution, and the surface morphology of the NC-modified-epoxy microstructures exhibit only minor deviations with respect to that of the unmodified reference material, as examined by means of microscopic and metrologic investigations. The proposed approach of the incorporation of emitting and non-bleachable NCs into a photoresist opens novel routes for surface patterning of integrated microsystems with inherent photonic functionality at the micro- and nanometer-scale for light sensing and emitting applications.