A three-dimensional neural probe electrode array system is described. Planar probes are microfabricated and electrically connected to flexible micro-machined ribbon cables using a rivet bonding technique. The distal end of each cable is connected to a probe with the proximal end of the cable being customized for connection to a printed circuit board. Final assembly consists of combining multiple such assemblies into a single structure. Each of the two-dimensional neural probe arrays is positioned into a micro-machined platform that provides mechanical support and alignment for each array. Lastly, a micro-machined cap is placed on top of each neural electrode probe and cable assembly to protect them from damage during shipping and subsequent use. The cap provides a relatively planar surface for attachment of a computer controlled inserter for precise insertion into the tissue.