A system and method are disclosed for the precision fabrication of Micro-Electro-Mechanical Systems (MEMS), Nano-Electro-Mechanical Systems (NEMS), Microsytems, Nanosystems, Photonics, 3-D integration, heterogeneous integration, and Nanotechology devices and structures. The disclosed system and method can also be used in any fabrication technology to increase the precision and accuracy of the devices and structures being made compared to conventional means of implementation. A platform holds and moves a substrate to be machined during machining and a plurality of lasers and/or ion beams are provided that are capable of achieving predetermined levels of machining resolution and precision and machining rates for a predetermined application. The plurality of lasers and/or ion beams comprises a plurality of the same type of laser and/or ion beam. Alternatively, a close-loop control system can be used with one laser or ion beam that is controlled and operated by the close-loop control system so as to achieve the predetermined levels of machining resolution and precision and machining rates for the predetermined application.