IR and Raman spectroscopy has been used to study the evolution of the vibrational spectrum of bundled single-walled carbon nanotubes (SWNTs) during the purification process needed to remove metal catalyst and amorphous carbon present in arc-derived SWNT soot. We have carried out a systematic study to define the different outcomes stemming from the purification protocol (e.g., DO, DO/HCl, DO/HNO₃, H₂O₂, H₂O₂/HCl), where dry oxidation (DO) or refluxing in H₂O₂ was used in a first purification step to remove amorphous carbon. The second step involves acid reflux (HCl or HNO₃) to remove the residual growth catalyst (Ni−Y). During strong chemical processing, it appears possible to create additional defects where carbon atoms are eliminated, the ring structure is now open, localized CC bonds are created, and O-containing groups can be added to this defect to stabilize the structure. Evolution of SWNT skeletal disorder obtained via chemical processing was studied by Raman scattering. Higher intensity ratios of R- and G-band (I_R/I_G) are more typically found in SWNT materials with low D-band intensity and narrow G-band components. Using IR transmission through thin films of nanotubes, we can resolve the structure due to functional groups that were present in the starting material or added through chemical processing. After high-temperature vacuum annealing of the purified material at 1100 °C, IR spectroscopy shows that most of the added functional groups can be removed and that the structure that remains is assigned to the one- and two-phonon modes of SWNTs.