Controlling individual atoms using lasers1, ion traps2 and scanning probe tips3 has transformed our understanding of matter and enabled breakthroughs in quantum science4–6. Extending this control into three-dimensional (3D) solids and across mesoscopic scales, however, remains a foundational challenge. Electron irradiation in electron microscopes is known to induce atomic displacements7, and atomic manipulation has been proposed8 and demonstrated9,10. Yet repeated and deterministic control has remained elusive9–17. Here we demonstrate deterministic atomic engineering in a 3D crystal, creating ordered arrangements of more than 40,000 user-defined defects within minutes across a 150 nm × 100 nm × 13 nm volume. By steering individual Cr atoms in the magnetic semiconductor CrSBr into selected interstitial sites using an electron beam directed with sub-20-pm-scale accuracy, we create vacancy–interstitial complexes. The resulting impurity array forms a mesoscale crystal embedded within the host lattice, a new form of engineered artificial matter that remains stable at room temperature and outside the microscope. By tracking Cr atom displacements, we identify conditions under which the defect structures are predictable. Our calculations suggest that these defects form correlated impurity states with intra-defect optical transitions and inter-defect kinetic and Coulomb interactions. This establishes a generalizable platform for atomic defect engineering at mesoscopic, and potentially macroscopic, scales, opening opportunities for scalable quantum technologies, including deterministic colour-centre placement, quantum simulation of many-body lattice models and atomic-scale manufacturing.
