In this paper, we investigate conjugated polymer layers structured by nanoimprint lithography toward their suitability for the fabrication of nanostructured polymer/metal sulfide hybrid solar cells. Consequently, we first study the thermal stability of the nanoimprinted conjugated polymer layers by means of scanning electron microscopy and grazing incidence small-angle X-ray scattering, which reveals a reasonable thermal stability up to 145 °C and sufficient robustness against the solvent mixture used in the subsequent fabrication process. In the second part, we demonstrate the preparation of nanostructured polymer/copper indium sulfide hybrid solar cells via the infiltration and thermal decomposition of a mixture of copper and indium xanthates. Although this step needs temperatures of more than 160 °C, the nanostructures are retained in the final polymer/copper indium sulfide layers. The nanostructured solar cells show significantly improved power conversion efficiencies compared to similarly prepared flat bilayer devices, which is based on a distinct improvement of the short circuit current in the nanostructured solar cells.