Plasma etching processes have been used for the past 30 years to shrink the pattern size of integrated devices. However, the inherent problems of plasma processes, such as ultraviolet photon radiation damage, limit the effectiveness of etching and surface treatments of nanoscale devices. To overcome these problems, we developed a neutral beam surface treatment process. The process uses neutral beams and a defect-free surface process to fabricate carbon nanotubes and self-assemble mono-layer devices. We found that neutral beams can be used to produce atomically defect-free surfaces in carbon nanotubes and organic molecules. This technique has potential for fabricating nanodevices.