The ability to create atomic-scale structures with the scanning tunneling microscope (STM) plays an important role in the development of a future nanoscale technology. I briefly review the various modes of STM-based fabrication and atomic manipulation I focus on using an ultrahigh vacuum STM to directly pattern the Si(001) surface by atomic manipulation Lit room temperature. By carefully adjusting the tip morphology and pulse voltage, a single atomic layer can be removed from the sample surface to define features one atom deep. Segments of individual dimer rows can be removed to create structures with atomically straight edges and with lateral features as small as one dimer wide. Trenches similar to 3 nm wide and 2-3 atomic layers deep can be created with less stringent control of patterning parameters. Direct patterning provides a straightforward route to the fabrication of nanoscale test structures under ultrahigh vacuum conditions of cleanliness.