In a method for processing a nanotube, a vapor is condensed to a solid condensate layer on a surface of the nanotube and then at least one selected region of the condensate layer is locally removed by directing a beam of energy at the selected region. The nanotube can be processed with at least a portion of the solid condensate layer maintained on the nanotube surface and thereafter the solid condensate layer removed. Nanotube processing can include, e.g., depositing a material layer on an exposed nanotube surface region where the condensate layer was removed. After forming a solid condensate layer, an electron beam can be directed at a selected region along a nanotube length corresponding to a location for cutting the nanotube, to locally remove the condensate layer at the region, and an ion beam can be directed at the selected region to cut the nanotube at the selected region.