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We present the local crystal structure control of multi- walled carbon nanotubes (MWNTs) by the irradiation of gallium ion beam (Ga+) and electron beam. The local crystal structure is evaluated by transmission electron microscope (TEM) and electron energy-loss spectroscopy (EELS). By controlling the dose rate of ion beam, the crystal structures of MWNTs can be changed from maintaining the layered shapes and amorphous shapes. By irradiating with low dose rate ion beam, the crystal structures of MWNTs hold the layered crystal structure (intermediate amorphous MWNT). We show that the crystal state was reconstructed as layered crystal stage from the intermediate amorphous MWNT by irradiating the electron beam. The fabricated nanostructures are expected to apply the various the mechanical or electrical components for nano-electro-mechanical systems.