Raman spectroscopy and mapping, coupled to molecular labelling, is used to analyse and monitor the first stage of carbon nanotube functionalization, i.e. their oxidation, which is usually performed to increase the number of surface carboxylic groups, allowing both a better dispersion in solution and the further attachment of biomolecules. Since the abundance of such surface groups is critical for the final application, it is important to develop a reliable but simple and fast method to investigate their presence on the tube walls. The presented data demonstrate the correlation between the presence and intensity of the Raman peak ascribed to the labelling molecule and the production of COOH groups on the nanotube walls. Between the analysed carbon nanotubes related spectral parameters, the G′ Raman peak position appears to be the most sensitive one to determine the degree of single walled carbon nanotube labelling, which directly depends on the number of COOH groups available for molecular attachment, i.e. on the efficiency of the oxidation treatment.