We report studies of bulk heterojunction solar cells composed of self-assembled poly(3-butylthiophene) nanowires (P3BT-nw) as the donor component with a fullerene acceptor. We show that the nanostructure of these devices is the single most important variable determining their performance, and we use a combination of solvent and thermal annealing to control it. A combination of conductive and photoconductive atomic force microscopy provides direct connections between local nanostructure and overall device performance. Films with a dense random web of nanowires cause the fullerene to aggregate in the interstices, giving a quasi-ordered interpenetrating heterojunction with high short-circuit current density (10.58 mA/cm2), but relatively low open circuit voltage (520 mV). Films with a low density of nanowires result in a random bulk heterojunction composed of small crystalline PCBM and P3BT phases. Fewer nanowires result in higher open circuit voltage (650 mV) but lower current density (6.02 mA/cm2). An average power conversion efficiency of 3.35% was achieved in a structure which balances these factors, with intermediate nanowire density. The best photovoltaic performance would be realized in a material structure which maintains the interpenetrating network of nanowires and fullerene phases (high current density), but avoids the device bridging we observe, and the recombination and shunt losses associated with it (high open-circuit voltage).