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We show that vertically aligned nanorod arrays composed of copper phthalocyanine (CuPc) molecules can be grown on various substrates using the oblique angle deposition technique in high vacuum. High-density nanorod arrays with diameters of 20-70 nm and spacing of 10-100 nm have been achieved with either stationary or rotated substrates. Scanning electron and atomic force microscopies are combined to study the morphology of CuPc nanorods grown under different conditions. X-ray diffraction reveals that the crystallinity of the CuPc nanorods is similar to a flat CuPc film deposited under normal molecular incidence. Interdigitated bulk heterojunctions (BHJs) have been formed by successfully infiltrating [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) to fill the spacing between the CuPc nanorods via spin coating. The resulted CuPc nanorod/PCBM photovoltaic cells possess a maximum power conversion efficiency approximately doubling that of bilayer CuPc/PCBM devices, demonstrating the effectiveness of the nanorod-based BHJ in enhancing both the donor-acceptor interfacial area and the exciton diffusion efficiency in the active layer.