In this study we use 25keV in situ and 30keV ex situ Ga+ focused ion beams (FIB) to locally modify the substrate before deposition to determine its affect on nucleation of MBE-grown Ge/Si islands. FIB processing may alter island formation in at least four ways: the surfactant effect of Ga+, doping effects of subsurface Ga+, crystalline damage, and surface roughening. To explore these possibilities, we milled square regions of increasing Ga+ doses and used AFM to monitor islanding in and around these regions. For in situ experiments, doses ranged from ∼1013 to 5×1017ions/cm2. We began to observe changes in island topology at doses as low as ∼1014ions/cm2. For doses of ∼1015ions/cm2 to ∼8×1016ions/cm2, implanted areas were surrounded by denuded zones that grew from ∼0.5 to 6 μm. Immediately inside the implanted area, island concentration (size and density) appeared to peak. At doses above ∼6×1016ions/cm2, 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 pre-growth cleaning and growth of a thin capping layer. Doses ranging from 7.5×1013 to ∼1017 ions/cm2 were used 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 show muted modifications for low Ga+ doses, while for higher doses trends similar to the in situ results are seen.