We report a comprehensive study involving the ion beam oxygen etching purification mechanism of domelike carbon nanostructures containing nitrogen. The CNx nanodomes were prepared on Si substrate containing nanometric nickel islands catalyzed by ion beam sputtering of a carbon target and assisting the deposition by a second nitrogen ion gun. After preparation, the samples were irradiated in situ by a low energy ion beam oxygen source and its effects on the nanostructures were studied by x-ray photoelectron spectroscopy in an attached ultrahigh vacuum chamber, i.e., without atmospheric contamination. The influence of the etching process on the morphology of the samples and structures was studied by atomic force microscopy and field emission gun-secondary electron microscopy, respectively. Also, the nanodomes were observed by high resolution transmission electron microscopy. The oxygen atoms preferentially bond to carbon atoms by forming terminal carbonyl groups in the most reactive parts of the nanostructures. After the irradiation, the remaining nanostructures are grouped around two well-defined size distributions. Subsequent annealing eliminates volatile oxygen compounds retained at the surface. The oxygen ions mainly react with nitrogen atoms located in pyridinelike structures. (C) 2008 American Institute of Physics.10312