Mesoscale atomic engineering in a crystal lattice

Controlling individual atoms using lasers¹, ion traps² and scanning probe tips³ has transformed our understanding of matter and enabled breakthroughs in quantum science^4-6. 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 demonstrated^9,10. Yet repeated and deterministic control has remained elusive^9-17. 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.