Polypyrrole (PPy) nanostructures (nanowires or nanotubes) were chemically synthesized inside an alumina template. The response surface methodology (RSM) based on central composite design (CCD) was used to determine the relationship between the morphology of the nanostructures (nanowires or nanotubes) and synthesis conditions. The concentrations of pyrrole, oxidant, time and temperature of the experiments were selected as independent variables. Using the results of experimental design, proper amount of reaction variables was selected in order to achieve desired morphology of PPy nanostructures. Monomer concentration in the range of 0.13–0.4M and 0.47–0.78M will result in the formation of nanotube and nanowire structures, respectively. Formation of nanotube and nanowire morphology was confirmed by Scanning Electron Microscope (SEM) analysis of the cross section of templates. The crystallographic and chemical structure of PPy nanowires was studied using XRD, UV–vis, Raman and FTIR spectroscopy. Electrochemical impedance spectroscopy (EIS) results show four order of magnitude decreases in the impedance of PPy nanostructure arrays rather than bare stainless steel sheet which makes PPy nanostructures suitable for use in neural microelectrodes surface modification.