This research presents a fabrication method of vertically aligned nanowires on substrates using lithography-assisted template bonding (LATB) towards developing highly efficient electrodes for biomedical applications at low cost. A polycarbonate template containing cylindrical nanopores is attached to a substrate and the nanopores are selectively opened with a modified lithography process. Vertically aligned nanowires are grown by electrochemical deposition through these open pores on polyimide film and silicon substrates. The process of opening the nanopores is optimized to yield uniform growth of nanowires. The morphological, crystalline, and electrochemical properties of the resulting vertically aligned nanowires are discussed using scanning electron microscopy (SEM), x-ray diffraction (XRD), and electrochemical analysis tools. The potential application of this simple and inexpensive fabrication technology is discussed in the development of neural probe electrodes.