In this study, we use 25 keV in situ and 30 keV ex situ Ga+ focused ion beams (FIBs) to locally modify the substrate before deposition and determine their effects on nucleation of molecular beam epitaxy grown Ge/Si islands. FIB processing may alter island formation in at least five ways: the surfactant effect of Ga+, doping effects of subsurface Ga+, local strains, crystalline damage, and surface roughening. To explore these possibilities, we milled square regions of increasing Ga+ doses and used atomic force microscopy to monitor islanding in and around these regions. For in situ experiments, doses ranged from similar to 10(13) to 5 X 10(17) ions/cm(2) (0.04-400 ML). We began to observe changes in island topology at doses as low as similar to 10(14) ions/cm(2). For doses of similar to 10(15) to similar to 8 X 10(16) ions/cm(2) (2-160 ML), implanted areas were surrounded by denuded zones that grew from similar to 0.5 to 6 mu m with increasing dose. Immediately inside the implanted area, island size and concentration appeared to peak. At doses above similar to 6 X 10(16) ions/cm(2) (120 ML), Ga+ produced noticeable surface depressions, which were often surrounded by enhanced island densities, rather than a denuded zone. For ex situ FIB patterning, samples underwent both pregrowth cleaning and growth of a thin capping layer (0-100 nm). Doses ranging from 7.5 X 10(13) to similar to 10(17) ions/cm(2) (0.15-200 ML) were used in concert with varied capping layer thicknesses to study their combined affect on island nucleation. The results correspond well with in situ experiments for thin capping layers. Increased capping layer thickness resulted in muted modifications to island formation for low Ga+ doses, while for higher doses trends similar to those obtained in situ are seen. (c) 2006 American Vacuum Society.