Vertically aligned carbon nanofibers (VACNFs) are grown directly on prefabricated electronic circuits with nanoscale precision. Utilizing the free-standing nanofiber array geometry, we have demonstrated the detection of nucleic acids to construct an ultrasensitive electrochemical sensor. Extending this technology towards in vivo applications, we have modified the free-standing VACNF arrays in order to achieve a multifunctional three dimensional (3-D) matrix that interpenetrates the neuronal network of PC12 cells. We found that PC12 cells cultured on the nanofiber arrays can form an extended neural network upon proper chemical and biochemical modification. The soft 3-D nanofiber array architecture provides a novel platform to fine-tune the topographical, mechanical, chemical, and electrical cues at sub-cellular scales. This biomaterial platform can be used for both fundamental studies of nanomaterial-cell interactions and the development of multifunctional, chronically stable implantable devices. The application of these devices and potential utility as a multifunctional platform for neurophysiology and biochemical studies will be discussed.