We describe an electrochemical method of directly growing conducting polymer nanostructures between metal electrodes with the geometry controlled by hydrophilic/hydrophobic patterns. The surface patterning can be achieved by a large number of lithographic methods such as AFM, electron-beam, elastomeric microprinting, and photolithography and is compatible with industrial semiconductor fabrication processes. Conducting polymer structures so formed have good alignment compared to bulk synthesis and are grown in place between electrodes. Polypyrrole field effect transistors have been produced using this method. Electrical measurements show conductivity strongly dependent on the presence of anionic dopant species during growth. Devices grown with a high concentration of dopant show metallic behavior, while those with less doping behave as p-type semiconductors.