There's a Micro Raman based study which shows that UV-sterilization is the best way to sterilize carbon nanotubes without altering their biological activity. Mohammad Hadi Norahan
"Micro-Raman study of the role of sterilization on carbon nanotubes for biomedical applications"
DOI: 10.2217/nnm.09.100
Having said that, carbon compounds having double bonds such as Fullerenes and carbon nanotubes often exhibit pro-oxidant activity on exposure to visible or UV-light. So you might have to check 2-3 methods to obtain the optimum strategy in your case.