Laser-assisted apparatus and methods for performing nanoscale material processing, including nanodeposition of materials, can be controlled very precisely to yield both simple and complex structures with sizes less than 100 nm. Optical or thermal energy in the near field of a photon (laser) pulse is used to fabricate submicron and nanometer structures on a substrate. A wide variety of laser material processing techniques can be adapted for use including, subtractive (e.g., ablation, machining or chemical etching), additive (e.g., chemical vapor deposition, selective self-assembly), and modification (e.g., phase transformation, doping) processes. Additionally, the apparatus can be integrated into imaging instruments, such as SEM and TEM, to allow for real-time imaging of the material processing.