The ability to inject dopant atoms with high spatial resolution, flexibility in dopant species, and high single ion detection fidelity opens opportunities for the study of dopant fluctuation effects and the development of devices in which function is based on the manipulation of quantum states in single atoms, such as proposed quantum computers. The authors describe a single atom injector, in which the imaging and alignment capabilities of a scanning force microscope (SFM) are integrated with ion beams from a series of ion sources and with sensitive detection of current transients induced by incident ions. Ion beams are collimated by a small hole in the SFM tip and current changes induced by single ion impacts in transistor channels enable reliable detection of single ion hits. They discuss resolution limiting factors in ion placement and processing and paths to single atom (and color center) array formation for systematic testing of quantum computer architectures in silicon and diamond. © 2008 American Vacuum Society.