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The multi-walled carbon nanotubes (MWCNTs) irradiated by N ion beams at different temperatures were investigated. At the irradiation dose of 1times1017 ions/cm2, the MWCNTs completely became amorphous at room temperature. The amorphous carbon of the N ion irradiated MWCNTs could be evaporated by 5 KeV focused electron beam irradiation. That is, the irradiated MWCNTs could be modified by the low energy electron beam irradiation. Nevertheless, with increasing the temperature, the radiation damage in MWCNTs that could destroy the structure was minimized. Moreover, at the temperature of 800 K, the interconnection of adjacent parallel MWCNTs could be realized at the irradiation dose of 1.5times1017 ions/cm2. This interconnection was ascribed to the fact that two adjacent MWCNTs shared a common graphene.