Highly aligned multi-wall carbon nanotubes were investigated with scanning electron microscopy (SEM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) before and after bombardment performed using noble gas ions of different masses (argon, neon and helium), in an ultra-high-vacuum (UHV) environment. Ion irradiation leads to change in morphology, deformation of the carbon (C) honeycomb lattice and different structural defects in multi-wall carbon nanotubes. One of the major effects is the production of bond distortions, as determined by micro-Raman and micro-X-ray photoelectron spectroscopy. We observe an increase in sp3 distorted bonds at higher binding energy with respect to the expected sp2 associated signal of the carbon 1s core level, and increase in dangling bonds. Furthermore, the surface damage as determined by the X-ray photoelectron spectroscopy carbon 1s core level is equivalent upon bombarding with ions of different masses, while the impact and density of defects in the lattice of the MWCNTs as determined by micro-Raman are dependent on the bombarding ion mass; heavier for helium ions, lighter for argon ions. These results on the controlled increase in sp3 distorted bonds, as created on the multi-wall carbon nanotubes, open new functionalization prospects to improve and increase atomic hydrogen uptake on ion-bombarded multi-wall carbon nanotubes.