Here, we report fluorination of multi-walled carbon nanotubes (MWNTs) via the surface wave microwave (SW-MW) plasma technique. We have investigated the change in the atomic and structures properties of fluorinated MWNTs using X-ray photoemission electron microscopy (XPS), Raman spectroscopy and transmission electron microscopy (TEM). The XPS study presents a semi-ionic boding character at a low concentration and a covalent bonding character at a high concentration. The Raman spectroscopy study shows an increase in disordered sp 3 hybridization in MWNTs with fluorine incorporation. High-resolution TEM study of fluorinated MWNTs shows an induced defect on the sidewall without affecting the inner tubes’ structure.