Three-dimensional electrode geometries were proposed to increase the spatial resolution in retinal prostheses aiming at restoring vision in blind patients. We report here the results from a study in which finite-element modeling was used to design and optimize three-dimensional electrode geometries. Proposed implants exhibit an array of well-like shapes containing stimulating electrodes at their bottom, while the common return grid electrode surrounds each well on the implant top surface. Extending stimulating electrodes and/or the grid return electrode on the walls of the cavities was also considered. The goal of the optimization was to find model parameters that maximize the focalization of electrical stimulation, and therefore the spatial resolution of the electrode array. The results showed that electrode geometries with a well depth of 30 µm yield a tenfold increase in selectivity compared to the planar structures of similar electrode dimensions. Electrode array prototypes were microfabricated and implanted in dystrophic rats to determine if the tissue would behave as hypothesized in the model. Histological examination showed that retinal bipolar cells integrate the electrode well, creating isolated cell clusters. The modeling analysis showed that the stimulation current is confounded within the electrode well, leading to selective electrical stimulation of the individual bipolar cell clusters and thereby to electrode arrays with higher spatial resolution.