Abstract: A method for cleaning or otherwise removing amorphous carbon and other residues that arise in growth of a carbon nanotube (CNT) array. The CNT array is exposed to a plurality of hydroxyls or hydrogen, produced from a selected vapor or liquid source such as H2O or H2O2, and the hydroxyls or hydrogen (neutral or electrically charged) react with the residues to produce partly or fully dissolved or hydrogenated or hydroxylizated products that can be removed or separated from the CNT array. The hydroxyls or hydrogen can be produced by heating the CNT array, residue and selected vapor or liquid source or by application of an electromagnetic excitation signal with a selected frequency or range of frequencies to dissociate the selected vapor or liquid. The excitation frequency can be “chirped” to cover a selected range of frequencies corresponding to dissociation of the selected vapor or liquid. Sonication may be used to supplement dissociation of the H2O and/or H2O2.