We report the integration of a scanning force microscope with ion beams. The scanning probe images surface structures non-invasively and aligns the ion beam to regions of interest. The ion beam is transported through a hole in the scanning probe tip. Piezoresistive force sensors allow placement of micromachined cantilevers close to the ion beam lens. Scanning probe imaging and alignment is demonstrated in a vacuum chamber coupled to the ion beam line. Dot arrays are formed by ion implantation in resist layers on silicon samples with dot diameters limited by the hole size in the probe tips of a few hundred nm.