The structure of individual multi-wall carbon nanotubes exposed to irradiation by a argon ions and electron flux, as well as subsequent heat processing in an inert medium has been studied using transmission electron microscopy and x-ray photoelectron spectroscopy. It has been shown that irradiation with argon ions and electrons leads to the formation of defects in the structure of carbon nanotubes, changes in the interlayer distance in the walls of nanotubes, and the fixing of functional oxygen-containing groups on their surface. Annealing of pre-irradiated nanotubes in an inert atmosphere causes a partial restoration of the multi-wall carbon nanotube structure. At the same time, in the case of irradiation with argon ions, the nanotube structure is being recovered and the oxygen concentration decreases. In the case of electron irradiation after annealing, extended multi-vacancy defects occur, on which functional groups containing a double chemical bond of carbon and oxygen (C=O) are formed. Using calculations carried out within the framework of density functional theory, the coupling energy values and optimized geometry for various configurations of vacancy clusters in the graphene plane have been obtained.