We report the details of an electron-beam-induced crystallization process of amorphous carbon. A high-resolution transmission electron microscope having a homemade nanomanipulator was used to observe defect repairing and the plastic deformation of a carbon nanotube caused by Joule heating. Electron irradiation at 200keV combined with 10μA Joule heating at 2V biasing voltage induced the crystallization of carbon nanocapsules from an amorphous carbon fibril. Further, a current exceeding 20μA caused defect repairing prior to plastic deformation in a multiwalled carbon nanotube. The outermost layer of the buckled multiwalled nanotube was repaired, but the buckled innermost layer retained its sharp angles as a result of plastic deformation.