Surface defects on highly oriented pyrolytic graphite (HOPG) were controllably produced by bombardment with Cs+ ions at various incident kinetic energies ranging from 0.3 to 10 keV and at various dose densities. Defects in the HOPG created by Cs+ ion impacts were subsequently oxidized at 650 °C in air to produce nanometer-size monolayer and multilayer molecule corrals (pits). The controlled production of both monolayer and multilayer pits on HOPG bombarded with energetic Cs+ ions was realized and studied by scanning tunneling microscopy (STM). The pit density, pit yield, pit diameter, and pit depth can be well controlled by varying the experimental conditions. Multilayer pits can be controllably produced using Cs+ ion bombardment at higher kinetic energies, and monolayer pits can be produced using low-energy Cs+ ion bombardment. The presence of both monolayer and multilayer pits on the same HOPG samples makes the direct comparison of pit growth rates possible under exactly the same conditions. The measured depth-resolved pit growth rates for multilayer pits are in good agreement with a model of the pit growth rate “acceleration” by adjacent layers, and the separate contributions to the pit growth rate of surface diffusion and collision were extracted.