We report on a new patterning technique for organic functional materials applicable to organic photovoltacis (OPVs). The unconventioal patterning technique, $O_2$ plsama-etching selectively perfluoro-alkyl fluorosilanes, is used for producing a bulk-heterojunction active layer with poly(3-hexylthiophene) as the electron donor and [6,6]-phenyl-$C_{61}$ butyric acid methyl ester as the electron acceptor. The patterning with reduced leakage path and parasitic capacitance suggests a way for fabrication of OPVs with higher energy conversion efficiency.