Direct-write processes enable the alteration or deposition of materials in a continuous, directable, sequential fashion. In this work, we demonstrate an electron beam direct-write process in an aberration-corrected scanning transmission electron microscope. This process has several fundamental differences from conventional electron-beam-induced deposition techniques, where the electron beam dissociates precursor gases into chemically reactive products that bond to a substrate. Here, we use elemental tin (Sn) as a precursor and employ a different mechanism to facilitate deposition. The atomic-sized electron beam is used to generate chemically reactive point defects at desired locations in a graphene substrate. Temperature control of the sample is used to enable the precursor atoms to migrate across the surface and bond to the defect sites, thereby enabling atom-by-atom direct writing.