The influence of the dwell-time in focused ion beam synthesis has been investigated. Cobalt disilicide layers have been produced by 70 keV Co2+ implantation into silicon and have been investigated by Rutherford backscattering spectroscopy and scanning electron microscopy. At an implantation temperature of about 400 °C it is only possible to form continuous CoSi2 layers using sufficiently short pixel dwell-times. This result is explained by an enhanced damage accumulation for longer dwell-times.