The surface chemistry of highly oriented pyrolytic graphite (HOPG) bombarded with energetic Cs+ ions was studied using the combined surface analysis techniques of TOF-SIMS (time-of-flight secondary ion mass spectrometry), XPS (X-ray photoelectron spectroscopy), and STM (scanning tunneling microscopy). Controlled surface modification of HOPG was achieved by bombardment of HOPG with Cs+ ions at various energies ranging from 0.24 to 10 keV and at various dose densities. The experimental findings suggest that cesium implanted into HOPG exists in an oxidized state, i.e,, in a form of cesium oxide. The Cs+ bombardment of HOPG enhances oxygen adsorption due to both the dissociative adsorption of oxygen at HOPG defect sires produced by Cs+ ions, and by the formation of cesium oxide. The surface coverage of cesium on HOPG increases linearly with increasing Cs+ dose density at low bombardment energies (less than or equal to 1 keV) and is independent of Cs+ dose density at high energies (greater than or equal to 3 keV), The surface coverage of cesium decreases rapidly with increasing Cs+ bombardment energy due to cesium implantation below the surface. The thermal stability of cesium in HOPG shows a complex behavior due to the competing effect of diffusion of cesium to, and desorption of cesium from. the HOPG surface at elevated temperatures. Defects in the HOPG created by the Cs+ ion bombardment can subsequently be the starting sites for O-2 oxidation at elevated temperatures, producing "molecule corral" pits. The controlled pit production by the thermal oxidation on Cs+ ion bombarded HOPG was realized and studied. The pit density, pit yield, and pit depth can be accurately controlled by varying Cs+ dose density and bombardment energy. The defects induced by energetic ion bombardment of HOPG provide a promising method for the production of "molecule corrals" in the control of the pit density, pit spatial distribution, and pit depth. Controlled pit production on ion-bombarded HOPG has promising potential applications both scientifically and technologically.