The emerging field of neuroprosthetics is focused on design and implementation of neural prostheses to restore some of the lost neural functions. Remarkable progress has been reported at most bioelectronic levels—particularly the various brain-machine interfaces (BMIs)—but the electrode-tissue contacts (ETCs) remain one of the major obstacles. The success of these BMIs relies on electrodes which are in contact with the neural tissue. Biological response to chronic implantation of Microelectrode arrays (MEAs) is an essential factor in determining a successful electrode design. By altering the material compositions and geometries of the arrays, fabrication techniques of MEAs insuring these ETCs try to obtain consistent recording signals from small groups of neurons without losing microstimulation capabilities, while maintaining low-impedance pathways for charge injection, high-charge transfer, and high-spatial resolution in recent years. So far, none of these attempts have led to a major breakthrough. Clearly, much work still needs to be done to accept a standard model of MEAs for clinical purposes. In this paper, we review different microfabrication techniques of MEAs with their advantages and drawbacks, and comment on various coating materials to enhance electrode performance. Then, we propose high-density, three-dimensional (3D), silicon-based MEAs using micromachining methods. The geometries that will be used include arrays of penetrating variable-height probes.