The conducting polymer polypyrrole (PPy) was electrochemically grown on hydrogel scaffolds deposited on the surface of microfabricated neural prosthetic devices. It is shown that the pyrrole monomer can be grown vertically through the hydrogel layer up to the surface without affecting the adjacent sites on the probes. The electrochemical properties of the conducting polymer-modified hydrogels were studied by impedance spectroscopy and cyclic voltammetry. It is also found that the conducting polymers could still be readily grown through the hydrogel after the microstructure is disrupted by freeze drying. Impedance measurements at the biologically important frequency of 1 kHz showed that the minimum impedance of this polymer-modified hydrogel was 7 kOmega. This is much lower than the minimum impedance of polypyrrole film ( approximately 100 kOmega).