The walls of nanotubes are inherently stable and relatively inert surfaces that have proven difficult to activate by chemical methods without damage. However, novel plasma methods have been developed that enable functionalization and doping of such inorganic nanomaterials in a controllable manner. This includes the first experimental demonstration of surface oxygen doping of boron nitride nanotubes (BNNTs), using an oxygen plasma. This allows testing of theoretical predictions that oxygen doping will change the optical, electric and magnetic properties of BNNTs. Selected functional groups have been attached to BNNTs as well as multiwalled carbon nanotubes (MWCNTs). For example, primary amines can be attached using either a N2+H2 plasma as well as plasma polymerization of heptylamine monomer. A combination of continuous wave and pulsed plasma modes has proven particularly effective at allowing selectable and controlled modification of nanotubes. This has allowed much better dispersion and bonding of nanotubes in composites, giving improved performance, and also allowed improved interfaces for biomedical applications. The combined plasma polymerization mode enabled production of a novel bio-interface on titanium, where osteoblast growth was enhanced and fibroblast cell growth was reduced. The same approach is to be applied to short nanotubes to potentially enable them to be used in drug delivery systems. Plasma methods also have potential for preparing nanotubes for use in solar cells, batteries/fuel cells, and sensors.