In recent years, high-resolution optical imaging in the far field has provided opportunities for alternative approaches to nanocharacterization traditionally dominated by electron and scanning probe microscopies. Here, we report the optical super-resolution imaging of model block copolymer (BCP) thin film surface nanostructures through stochastic optical reconstruction microscopy (STORM). We compare a set of surface-functionalized fluorescent core-shell silica nanoparticles encapsulating two different organic dyes, Cy3 and Cy5, with the corresponding free dyes in STORM. Using various click-type chemistries, these probes are covalently attached to the surface of specific blocks of BCP thin films, enabling selective block labeling and optical visualization. We demonstrate that the enhanced brightness of these particle probes offers distinct advantages over conventional dye labeling, outperforming one of the best STORM dyes available (Cy5).