A strategy to fabricate nanostructured poly(3-hexylthiophene) (P3HT) films for organic photovoltaic (OPV) cells by a direct transfer method from a reusable soft replica mold is presented. The flexible polyfluoropolyether (PFPE) replica mold allows low-pressure and low- temperature process condition for the successful transfer of nanostructured P3HT films onto PEDOT/PSS-coated ITO substrates. To reduce the fabrication cost of masters in large area, we employed well-ordered anodic aluminum oxide (AAO) as a template. Also, we provide a method to fabricate reversed nanostructures by exploiting the self-replication of replica molds. The concept of the transfer method in low temperature with a flexible and reusable replica mold obtained from an AAO template will be a firm foundation for a low-cost fabrication process of ordered OPVs.