The reaction of 5-20 eV O+ with highly oriented pyrolytic graphite (HOPG) is investigated under ultrahigh vacuum (UHV) conditions. Ion induced modifications of HOPG are characterized in situ by X-ray photoelectron spectroscopy (XPS) and temperature programmed desorption (TPD) at various stages during exposure to O+. The incident energy of O+ ions is found to be positively correlated with the rate of oxygen uptake and negatively correlated with oxygen coverage in the steady state. In addition, three oxygen containing species are detected on HOPG, namely, C-O-C, O=C and HO-C=O. The variation of these species on graphite is monitored as a function of O+ dose and heating temperature. Ion-induced modifications of the graphite surface are monitored ex-situ by scanning tunneling microscopy (STM) with a variety of doses of impinging ions. The probability of defect initiation at room temperature is estimated and compared between O+ and Ne+ ions with different incident energies. Graphite etching efficiency is also compared between 5-eV O+ and O atom. A monolayer of mercaptopropylisobutyl-POSS on Au(111) is characterized by STM and atomic force microscope (AFM). Ion induced modifications of the POSS monolayer are monitored in situ by XPS. During O+ exposure, isobutyl side groups are continuously depleted from the surface, while the silicon concentration is kept constant and SiO2 is formed on the Au substrate. After prolonged O+ exposure, the gold surface eventually becomes oxidized but the oxide can be removed by annealing at 180 oC. The oxidation resistance of the POSS monolayer is compared with that of a dodecanethiol/Au(111) self-assembled monolayer (SAM).