Microelectrode arrays are commonly used for electrophysiological neural recording from individual neurons in the brain to study neural pathway or to form an interface between brain and machine. However, it is also known that the electrode implantation into the brain often induces immunological tissue response around the electrode array, limiting the long-term neural recording. Since the diameter of carbon fiber can be much smaller than that of conventional microwires, carbon fiber based electrodes can reduce the response of glial response. In the present study, we proposed a carbon fiber based microelectrode array embedded with mechanical support structure to facilitate penetration into the deeper brain. The support is made of biodegradable silk fibroin to reduce the reactive responses. 4 channel carbon fiber based microelectrode arrays were fabricated and evaluated for electrochemical impedance, long term neural recording capability and immunohistochemical analysis for 1 month implantation in the rat brains.