A vertically aligned peptide nanowire film, prepared by the self-assembly of diphenylalanine upon exposure to fluorinated aniline vapor at high temperature, exhibits a superhydrophobic property due to its nanoscale roughness and low surface free energy. We fabricated a self-cleaning, superhydrophobic surface by hierarchically re-organizing peptide nanowires into a hill-and-valley-like structure using capillary force induced by solvent-evaporation. Our approach provides an alternative way of nanofabrication for superhydrophobic materials, which should broaden the spectrum of applications for peptide self-assembly.