This paper presents a novel microelectrode arrays using high-temperature grown vertically aligned carbon nanotubes (CNTs) integrated on a flexible and biocompatible parylene substrate. A simple microfabrication process is proposed to unite the high quality vertical CNTs grown at high temperature with the heat sensitive parylene substrate in a highly controllable manner. Briefly, the CNTs electrode is encapsulated by two layers of parylene and the device is released using xenon difluoride (XeF2). The process is compatible with wafer-scale post complementary metal oxide semiconductor integration. Lower impedance and larger interfacial capacitance have been demonstrated using CNTs compared to a Pt electrode. The flexible CNT electrodes have been utilized for extracellular neuronal recording and stimulation in rats. The signal-to-noise ratio of the device is about 12.5. The threshold voltage for initiating action potential is about 0.5 V.