Pristine, oxidized and defunctionalized carbon nanotubes (CNTs) were studied by Raman spectroscopy, X-ray diffraction, transmission electron microscopy and low temperature nitrogen adsorption. The Raman spectra of the studied samples in the range of 900-1800 cm-1 were deconvoluted into five components to reveal the CNT oxidation mechanism. It was found that the oxidation resulted in the reduction of graphite components and ordering of both the structured and defect part of CNTs. Acid treatment also led to different types of disorders in the surface layers of CNTs. Polyene-type, polyphenylene-type and turbostratic fragments were detected as a result of partial exfoliation. Investigation of defunctionalized CNTs showed the ordering of edge carbon atoms as well as the invariability of the total amount of defects. The study of CNTs as supports for Co-based catalysts revealed a simultaneous decrease in the number of defect fragments and increase in the number of edge carbon atoms during catalyst preparation and reduction.