An electronic microarray has been used to carry out directed self-assembly of higher order 3D structures from Biotin/Streptavidin and DNA derivatized nanoparticles. Structures with up to fifty layers of alternating biotin and streptavidin and DNA nanoparticles were fabricated using a 400 site CMOS microarray system. In this process, reconfigurable electric fields produced by the microarray device were used to rapidly transport, concentrate and accelerate the binding of 40 nanometer biotin, streptavidin and DNA derivatized nanoparticles to selected sites on the microarray. The nanoparticle layering process takes less than one minute per layer (10-20 seconds for addressing and binding nanoparticles, 40 seconds for washing). The nanoparticle addressing/binding process was monitored by changes in fluorescence intensity as each nanoparticle layer was deposited. The final multilayered 3-D structures are about two microns in thickness and 50 microns in diameter. Active structures with chemical to luminescent to fluorescent properties are now being fabricated. The use of a microelectronic array device for assisted self-assembly represents a unique example of combining "top-down" and "bottom-up" technologies into a unique nanofabrication process. Such a process will be useful for the hierarchal assembly of 3D nano, micro, and macrostructures for a variety of electronic/photonic, nanomaterials, energy and biosensor applications.