Vertically aligned carbon nanotubes were grown over the inner wall of the pores of an anodic aluminum oxide template via chemical vapor deposition. The versatile approach of bipolar electrochemistry was generalized to modify the tubes selectively on one end with an organic layer of 4-aminobenzene moieties. The presence of the template during the bipolar experiments intrinsically protects the tubes' outer surface from the grafting of the organic layer. The layer is thus not only selectively grafted at the cathodic side of the tubes, but also exclusively onto the tubes' inner surface. For longer deposition times, the end of the tubes was completely capped with a dense organic layer. Thus bipolar electrochemistry can not only generate CNTs bearing organic functionalities on the tube surface for bio-sensing or bio-electrocatalytic applications, but can also create a dense organic layer as a cap at one end of the tubes, opening up applications in the fields of drug storage and delivery.