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In this work we report a simple procedure to anneal multiwalled carbon nanotubes (MWCNTs) under 20 KeV electron beam irradiation. MWCNTs synthesized using a chemical vapour deposition procedure are radially deformed and have catalyst impurities. They have a tendency to form parallel bundles of tubes, and this bundling process has been observed in real time. Scanning electron spectroscopy (SEM) and Raman spectroscopy (RS) are used to probe the structure of MWCNTs before and after annealing. The electron beam not only is used to locally anneal nanotubes and remove defects but also functionalizing them oxygen containing groups, this estimated by in situ SEM and EDS investigations. In previous reports heating above 1500 0C was required to anneal defects in bulk multiwalled nanotubes. The purity of MWCNTs was characterized by the intensity ratio of D-band to G-band (ID/IG), which was 1.07 and 0.74 for pristine and annealed MWCNTs, respectively. Annealed MWCNTs have greater surface area than the pristine one, which improves filterability applications. To investigate the filtration performance of MWCNTs irradiated by electron beam, the removal of Cr (VI) from aqueous solutions was studied as a function of Cr(VI) ion concentration, pH, MWCNT mass. It was found that annealed MWCNTs filters are more efficient to remove Cr(VI) from aqueous solutions. We therefore conclude that electron beam irradiation provides a novel approach to modify MWCNTs and significantly enhances their filtration efficiency. The reversibility of Cr(VI) adsorption onto MWCNTs by desorption process was also discussed.