We present a combined experimental and simulation approach to studying the primary damage caused by ion irradiation. We have examined a surface of copper subjected to 500 eV Ar+ ion bombardment using scanning tunnelling microscopy (STM) and observed craterlike regions of damage, with a central hole surrounded by adatoms. Molecular dynamics (MD) simulations reproduce this structure and enable us to study the formation process. We find both qualitative and quantitative agreement between the defect structures observed in STM and MD, providing a rare direct validation of the MD simulation. We observe a process in which a stress wave produces defect clusters fully formed at the surface, in contrast to the conventional bulk picture of creation, migration, and aggregation of point defects. This produces a characteristic crater structure. We also observe one-dimensional stress propagation events, which produce defects far from the initial collision and cooling of the thermal spike without self diffusion.