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Fluorination is effective in chemically modifying and controlling physicochemical properties of carbon materials over a wide range so creating opportunities to prepare carbon alloys with new functionalities. Carbon alloyed nanotubes were prepared by selective fluorination of hidden surfaces of multi-wall carbon nanotubes using a template carbonization technique. Carbon–fluorine bonds are formed on the hidden surfaces of the tubes while internal surfaces retained their sp2-hybridization. Fluorination (as a form of carbon-alloying) significantly affects such properties of hidden surface extents of nitrogen adsorption, hysteresis loops and pore size distributions. Fluorination enhanced the coulomb efficiency of Li/carbon nanotube rechargeable cells in an aprotic medium (with reversible lithium insertion in hidden surfaces) as studied by galvanostatic discharge-charge experiments.