Free-standing nanorod arrays of poly(3-hexylthiophene) (P3HT) were fabricated on indium tin oxide/glass substrates using anodic aluminum oxide (AAO) templates. The AAO templates were treated with a low molecular weight polydimethylsiloxane mold-release agent to reduce their surface energy of the template and interactions with the P3HT. Using a thermal nanoimprinting process, the templates were easily removed, generating nanorods on the surfaces of P3HT thin films. These unique structures were investigated for application in organic photovoltaic devices