The nanoscale morphology in polymer:PCBM based photovoltaic devices is a major contributor to overall device performance. The disordered nature of the phase-separated structure, in combination with the small length scales involved and the inherent difficulty of reproducing the exact morphologies when spin-coating and annealing thin blend films, have greatly hampered the development of a detailed understanding of how morphology impacts photovoltaic device functioning. In this paper we demonstrate a double nanoimprinting process that allows the formation of nanostructured polymer:PCBM heterojunctions of composition and morphology that can be selected independently. We fabricated photovoltaic (PV) devices with extremely high densities (1014 mm−2) of interpenetrating nanoscale columnar features (as small as 25 nm; at or below the exciton diffusion length) in the active layer. By comparing device results of different feature sizes and two different polymer:PCBM combinations, we demonstrate how double imprinting can be a powerful tool to systematically study different parameters in polymer photovoltaic devices.