The annealing behavior of Si(111)-7 × 7 surface defects created by Xe ion irradiation has been studied by a variable temperature scanning tunneling microscope (VT-STM). When Xe ions were irradiated on the Si surface at room temperature, traces with a diameter of a few nanometers could be observed on the surface. After 400°C annealing, defects formed in the Si substrate diffused toward the surface, and new vacancies appeared on the surface. Upon annealing to 600°C, the small vacancy clusters moved on the surface during annealing and were absorbed by large vacancy clusters. Thus, larger vacancy clusters were formed whose size corresponded to the number of defects created in the shallow surface region of the Si substrate. In addition, ion irradiation effects on nucleation and growth of Ge atoms deposited have been studied. For the growth of Ge islands on the Si surface without Xe ion irradiation, the density and the area of the islands increased with increase of deposition time. On the other hand, in the case of using Si substrates irradiated by Xe ions, followed by annealing, Ge islands were formed near the vacancies on the surface. It was found that these vacancies act as the nucleation sites for Ge deposition. Furthermore, to be compared with the case of the Si surface without Xe ion irradiation, the island density was higher and the area of the island was smaller. © 2002 Elsevier Science B.V. All rights reserved.