We show that electron irradiation in a dedicated scanning transmission microscope can be used as a nano-electron-lithography technique allowing the controlled reshaping of single walled carbon and boron nitride nanotubes. The required irradiation conditions have been optimized on the basis of total knock-on cross sections calculated within density functional based methods. It is then possible to induce morphological modifications, such as a local change of the tube chirality, by sequentially removing several tens of atoms with a nanometrical spatial resolution. We show that electron beam heating effects are limited. Thus, electron beam induced vacancy migration and nucleation might be excluded. These irradiation techniques could open new opportunities for nanoengineering a large variety of nanostructured materials.