We studied the oxygen etching of individual single-walled carbon nanotubes on silicon oxide substrates using atomic force microscopy and high-temperature environmental scanning electron microscopy. Our in situ observations show that carbon nanotubes are not progressively etched from their ends, as frequently assumed, but disappear segment by segment. Atomic force microscopy, before and after oxidation, reveals that the oxidation of carbon nanotubes on substrates proceeds through a local cutting that is followed by a rapid etching of the disconnected nanotube segment. Unexpectedly, semiconducting nanotubes appear more reactive under these conditions than metallic ones. We also show that exposure to electron and laser beams locally increases the chemical reactivity of carbon nanotubes on such substrates. These results are rationalized by considering the effect of substrate-trapped charges on the nanotube density of states close to the Fermi level, which is impacted by the substrate type and the exposure to electron and laser beams.