Neural prosthetics, which are increasingly being considered for the dual functionalities of recording and stimulation, are implanted in a corrosive biochemical environment that requires them to possess superior electrical and electrochemical stability and performance. These probes are required to withstand these operating conditions through billions of cycles of pulses of electrical stimulations and also maintain electrochemical sensitivity for potential applications in voltammetry. In this research, microelectrodes made of two material systems; namely, platinum and glassy carbon, supported on a flexible substrate are fabricated and investigated for correlation between process parameters and the electrochemical efficacy of the neural interfaces, particularly charge storage capacity and corrosion rate. Using scanning electron and atomic force microscopies, the correlation between process parameters, surface morphology and topography in both platinum and glassy carbon were investigated. The results demonstrate that changes in surface topography and the rate of corrosion are correlated to variations in the process parameters. Furthermore, the results indicate a relationship between surface roughness and corrosion rate, in which the increase or decrease of the former corresponds to a similar change in the latter.