Multi-walled carbon nanotubes (MWCNTs) were irradiated with focused electron beams in a transmission electron microscope at room temperature. The results showed that carbon nanotubes had no obvious structural damages but only shell bending under 100 keV electron beam irradiation. However, when the electron energy increased to 200 keV, the nanotubes were damaged and amorphization, pits and gaps were detected. Furthermore, generating of carbon onions and welding between two MWCNTs occurred under 200 keV electron irradiation. It was easy to destroy the MWCNTs as the electron beams exceeded the displacement threshold energy that was calculated to be 83-110 keV. Conversely, the energy of electron beams below the threshold energy was not able to damage the tubes. The damage mechanism is sputtering and atom displacement.