A system and method for manipulating and processing nanowires in solution with arrays of holographic optical traps. The system and method of the present invention is capable of creating hundreds of individually controlled optical traps with the ability to manipulate objects in three dimensions. Individual nanowires with cross-sections as small as 20 nm and lengths exceeding 20 μm are capable of being isolated, translated, rotated and deposited onto a substrate with holographic optical trap arrays under conditions where single traps have no discernible influence. Spatially localized photothermal and photochemical processes induced by the well-focused traps can also be used to melt localized domains on individual nanowires and to fuse nanowire junctions.