Here, a colloidal templating procedure for generating high-density arrays of gold macroporous microwells, which act as discrete sites for surface-enhanced Raman scattering (SERS), is reported. Development of such a novel array with discrete macroporous sites requires multiple fabrication steps. First, selective wet-chemical etching of the distal face of a coherent optical fiber bundle produces a microwell array. The microwells are then selectively filled with a macroporous structure by electroless template synthesis using self-assembled nanospheres. The fabricated arrays are structured at both the micrometer and nanometer scale on etched imaging bundles. Confocal Raman microscopy is used to detect a benzenethiol monolayer adsorbed on the macroporous gold and to map the spatial distribution of the SERS signal. The Raman enhancement factor of the modified wells is investigated and an average enhancement factor of 4 × 104 is measured. This demonstrates that such nanostructured wells can enhance the local electromagnetic field and lead to a platform of ordered SERS-active micrometer-sized spots defined by the initial shape of the etched optical fibers. Since the fabrication steps keep the initial architecture of the optical fiber bundle, such ordered SERS-active platforms fabricated onto an imaging waveguide open new applications in remote SERS imaging, plasmonic devices, and integrated electro-optical sensor arrays.