The tendency of freshly cleaved highly oriented pyrolytic graphite (HOPG) to form nanometer-sized circular pits during high temperature oxidative etching is an example of a controllable, nanoscale tailoring of a surface with a number of potential applications. Here we explore the possibility of modulating the number density, shapes, and dimensions of such etch pits by deliberately nucleating defects at or near the surface by bombardment with kilo-electronvolt polyatomic projectiles. We observed that bombardment of HOPG by 176 keV apomyoglobin ions resulted in the nucleation of a large population of deep hexagonal etch pits upon baking. The depths of the pits also give new information on the depth to which a material is damaged by impinging energetic polyatomic projectiles.