Vertically aligned carbon nanofiber (VACNF) is a promising electrode structure for electrochemical biosensor platform. In this paper, we address the mechanical stability and reusability issues of VACNF arrays. We demonstrate that improvement in mechanical stability requires special attention to surface treatment. We show that a thin SU8 layer on nanofiber forest forms a flexible passive layer at the base of the array and that wet etching works best to remove the passive layer from the VACNF tips. The optimum time for wet etching was found to be 2–3 minutes. We show that SU8 treated VACNF arrays have improved signal-to-noise response compared to the untreated bare VACNF arrays.