Nanoimprint lithography is used to directly pattern the conjugated polymer semiconductor poly(3-hexylthiophene) (P3HT). We obtain trenches with aspect ratios up to 2 and feature sizes as small as 50 nm in this polymer. The application to organic solar cells is shown by creating an interpenetrated donor-acceptor interface, based on P3HT and N,N'-ditridecyl-3,4,9,10-perylenetetracarboxylic diimide (PTCDI-C(13)), deposited from the vapor phase to reduce shadow effects. A planarizing layer of spin-coated zinc oxide (ZnO) nanoparticles is used to reduce the roughness of the layer stack. The response of the photovoltaic devices follows the increased interface area, up to a 2.5-fold enhancement.