CuPc nanorod growth was investigated on ITO substrates with and without 1H,1H,2H,2H-perfluoro-noctylphosphonic acid (FOPA) SAM modification, using vapor phase deposition, through the control of the temperature and surface energy of ITO substrates. At a substrate temperature of 200 degrees C, copper phthalocyanine (CuPc) thin films that composed nanorods were prepared on both substrates. On FOPA-ITO, it was suggested that CuPc molecules were stacked with an edge-on orientation because of the dominant intermolecular - interaction through the decrease of surface energy of ITO with FOPA modification. Organic photovoltaic cells containing CuPc nanorods as a p-type semiconductor were fabricated and photovoltaic characteristics were observed.