Methods, devices, and systems for forming atomically precise structures are provided. In some embodiments, the methods, devices, and systems of the present disclosure utilize a scanning tunneling microscope (STM) to remove portions of a monolayer of atoms or molecules from a crystalline surface to form atomically precise structures. The STM is utilized to both image the sample and remove the desired portions of the monolayer of atoms or molecules. In some instances, the lattice structure of the crystalline surface is utilized as a coordinate system by a control system of the STM to facilitate the automated removal of specific atoms or molecules from the crystalline surface.