The Electron Cyclotron Resonance (ECR) plasma is a relatively new and scalable technique which opens up possibilities for a more environmentally friendly and rapid method of nanotube purification. We report a single step, dual purification and functionalisation technique using nitrogen-ECR plasma and compare results to those from standard RF plasma via Raman, Thermal Gravimetric Analysis (TGA), X-ray Photon spectroscopy (XPS) and static contact angle measurement. The purity of the nanotubes was evaluated by TGA which showed »96% for the N-ECR treated and »91% for the N-CCRF. Defects introduced by plasma exposure acted to functionalise the nanotubes by nitrogen attachment as evidenced by Raman, XPS and static contact angle measurements. The impact of nitrogen ion bombardment with two different plasma ion energies is fingerprinted by the defects induced in the nanotube matrix.