Improved methods of functionalizing the surfaces of multi-walled carbon nanotubes (MWCNTs) have been investigated. It is shown that a level of primary amines of 2.3%, higher than previously reported for any nitrogen-containing gas plasma treatment, can be achieved using a mixture of N2 and H2, which is preferable to using NH3. Even higher levels (3.5%) of primary amines can be achieved by coating the MWCNTs with a thin layer of plasma polymerized heptylamine. In both cases, the highest levels were achieved using a combined continuous plus pulsed plasma mode which was superior to either continuous wave or pulsed wave alone. The integrity of the MWCNT structure is maintained by the plasma treatments, and the functionalized surface improves the dispersion of the MWCNTs and their interfacial bonding with epoxy, giving superior nanoindentation performance of the composites.