AbstractAtomic and close-to-atom scale manufacturing is a promising avenue toward single-photon emitters, single-electron transistors, single-atom memory, and quantum-bit devices for future communication, computation, and sensing applications. Laser manufacturing is outstanding to this end for ease of beam manipulation, batch production, and no requirement for photomasks. It is, however, suffering from optical diffraction limits. Herein, we report a spatial resolution improved to the quantum limit by exploiting a threshold tracing and lock-in method, whereby the two-order gap between atomic point defect complexes and optical diffraction limit is surpassed, and a feature size of <5 nm is realized. The underlying physics is that the uncertainty of local atom thermal motion dominates electron excitation, rather than the power density slope of the incident laser. We show that the colour centre yield in hexagonal boron nitride is transformed from stochastic to deterministic, and the emission from individual sites becomes polychromatic to monochromatic. As a result, single colour centres in the regular array are deterministically created with a unity yield and high positional accuracy, serving as a step forward for integrated quantum technological applications.