In the present study high dose 50 eV Ne and Kr ion implantation were used to remove nanosize cavities in (1 0 0) monocrystalline silicon. Nanosize cavities were created by 30 keV 3He implantation with a dose of 5 × 10 16 cm −2 and subsequent annealing in vacuum at 1100 K. Only in the case of Ne irradiation the cavities were filled up with self-interstitials generated at the surface by Ne ions. The implantation temperature was kept at about 600 K to avoid formation of irradiation defects in the near surface region. The Ne implantation dose varied from 10 18 to 3 × 10 19 cm −2. The size and the location of the clusters before and after Ne implantation were determined by the variable energy positron annihilation (VEP) technique. The evolution of the helium-vacancy clusters during all the experimental treatments of the samples, including 30 keV helium implantation, 1000 K annealing and Ne implantation, was simulated using the Monte-Carlo program MODEX. Reasonable agreement was obtained between the simulated and experimentally observed results, suggesting that the physical model used in the simulation is correct.