Atomic manipulation with the scanning tunneling microscope offers a method for patterning with nanometer-scale resolution in the ultraclean environment available in ultrahigh vacuum. We have used atomic manipulation to write nanoscale trenches in Si(001) surfaces and thus define structures that have atomically straight edges. These experiments suggest that silicon films can be directly patterned with atomic resolution for films that are one atomic layer thick and with 2.4 nm resolution for films that are three atomic layers thick. We report on the growth and patterning of single atomic layers of electronic materials on Si(001).