Using scanning tunneling microscopy, we have investigated vacancy-mediated, layer-by-layer removal of surface atoms from Si(111) under 225-eV Xe-ion bombardment. We observe, with increasing substrate temperature, both the transition from vacancy-cluster nucleation to step retraction, and a transition from disruption to preservation of the 7\ifmmode\times\else\texttimes\fi{}7 reconstruction on exposed material. We discuss the consequences of these observations for ion-beam-mediated epitaxy.