We developed focused ion beam direct deposition as a new method for fabricating patterned metal films directly on substrates. We designed and constructed a focused ion beam apparatus which satisfied demanded capabilities for direct deposition such as low energy and fine focused beam, high beam current density, high vacuum condition, changeability of ion species, precise and wide range patterning, sample observation by an optical microscope, and quick sample exchange. We also developed liquid alloy–metal ion sources for conductive materials, superconductive material and magnetic material. We tried to apply the focused ion beam direct deposition method to IC modification, surface acoustic wave (SAW) devices, SQUIDs, multilayers, and probing on small crystals. In SAW devices, SQUIDs, and multilayers, fabricated devices had comparable performance to devices fabricated by ordinary photolithographic processes. In IC modification and probing on small crystals, a low resistant and flexible connection was confirmed. We proved that focused ion beam direct deposition method is a useful tool for research and development such as prototyping.