The long-term performance of neural microelectrodes relies on biocompatibility and sensitivity of the electrode-tissue interface. Current neural electrodes are limited by poor electrical performance including high initial impedance and low charge storage capacity. In addition, they are mechanically hard which causes cellular reactive response to the implanted electrode. In this report, we have demonstrated a new templating method for fabrication of highly aligned conducting polymer nanotube. The structure of nanotubes can be precisely modulated by varying the time of electropolymerization. The electrical performance of poly(pyrrole) (PPY) and poly(3,4-ethylenedioxythiophine) (PEDOT) nanotubes including impedance and charge storage capacity were studied and compared as the surface morphology and structure of nanotube varied during the fabrication process. PEDOT nanotubes were found to have lower impedance than PPY nanotubes. By contrast, PPY nanotubes were shown to have higher charge storage capacity. These finding suggest that aligned conducting polymer nanotubes may enhance the long-term performance of neural microelectrodes.