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We use thermal and room temperature nanoimprint lithography (NIL) for directly patterning the photoactive polymer poly(3-hexylthiophene-2,5-diyl) (P3HT) in the sub-50-nm region. Different types of molds were used to directly imprint the desired structures into P3HT thin films. Good pattern transfer is achieved independent of the presence of other underlying polymer layers or the type of substrate incorporated. Further, we discuss the future application of this technology to the fabrication of ordered heterojuction organic photovoltaic devices and demonstrate that the NIL process involved does not damage the polymer or alter its chemical or electrical properties.