Controlled introduction of defects into aligned multiwalled carbon nanotubes (MWCNTs) was achieved by time-dependent plasma etching. The subsequent morphological changes in MWCNTs have been fingerprinted using Raman and x-ray photoelectron spectroscopy, by which induction of defects by functionalization was confirmed. We found that the introduction of defects along the nanotube body affects all Raman vibrational modes. A systematic analysis of the relationship between D, D′, D*, and G modes leads us to believe that no one peak can be used as an accurate standard for estimation of defects in nanotubes.