A low-energy focused ion beam system which is combined with molecular beam epitaxy apparatus was developed. Focusing characteristics were estimated by secondary electron and transmitted ion images. Using this system, the direct deposition of Au and Si was performed, which is important for in situ contact formation. Film purity was measured by Auger electron spectroscopy. Results show that the amount of impurities inside the him depends both on the deposition rate and on the chemical property of the deposition material.