The functionalization of multi-walled carbon nanotubes (MW-CNTs) was obtained by generating reactive perfluoropolyether (PFPE) radicals that can covalently bond to MW-CNTs’ surface. Branched and linear PFPE peroxides with equivalent molecular weights of 1275 and 1200 amu, respectively, have been thermally decomposed for the production of PFPE radicals. The functionalization with PFPE chains has changed the wettability of MW-CNTs, which switched their behavior from hydrophilic to super-hydrophobic. The low surface energy properties of PFPEs have been transferred to MW-CNTs surface and branched units with trifluoromethyl groups, CF3, have conferred higher hydrophobicity than linear units. Porosimetry discriminated the effects of PFPE function...