Surface nanobubbles forming on hydrophobic surfaces in water present an exciting opportunity as potential agents of top-down and bottom-up nanopatterning. The formation and characteristics of surface nanobubbles are strongly influenced by the physical and chemical properties of the substrate. In this study, focused ion beam (FIB) milling is used for the first time to spatially control the nucleation of surface nanobubbles with 75 nm precision. The spontaneous formation of nanobubbles on alternating lines of a self-assembled monolayer (octadecyltrichlorosilane) patterned by FIB is detected by atomic force microscopy. The effect of chemical vs topographical surface heterogeneity on the formation of nanobubbles is investigated by comparing samples with OTS coating applied pre-vs post-FIB patterning. The results confirm that nanoscale FIB-based patterning can effectively control surface nanobubble position by means of chemical heterogeneity. The effect of FIB milling on nanobubble morphology and properties, including contact angle and gas oversaturation, is also reported. Molecular dynamics simulations provide further insight into the effects of FIB amorphization on surface nanobubble formation. Combined experimental and simulation investigations offer insights to guide future nanobubble-based patterning using FIB milling.