For the combination of unique structure, dimension, strength, chemical stability, and electronic properties, carbon nanotubes (CNTs) are very important materials. However, CNTs from commercial sources usually contain some impurities, such as amorphous carbon, metallics, which are usually eliminated by some purification processes that includes reflux in acids and strong oxidation. This strong chemical procedure may damage the nanotube properties and it is thus important to control the extent of oxidation during the purification procedure. In this study, we provide a comprehensive study of the structure and physical composition of CNTs during each step of the purification process. Techniques such as scanning electron microscopy and Infrared spectroscopy were used to track the CNTs structure, in terms of length and diameter distribution, and surface chemical modifications during each purification stage.