The high-efficiency preparation of large-area microstructures of optical materials and precision graphic etching technology is one of the most important application directions in the atomic and near-atomic-scale manufacturing industry. Traditional focused ion beam (FIB) and reactive ion etching (RIE) methods have limitations in precision and efficiency, hindering their application in automated mass production. The pulsed ion beam (PIB) method addresses these issues by enhancing ion beam deflection to achieve high-resolution material removal on a macro scale, which can reach the equivalent removal resolution of 6.4 × 10⁻⁴ nm. Experiments were conducted on a quartz sample (10 × 10 × 1 mm) with a specific pattern mask using the custom PIB processing device. The surface morphology, etching depth, and roughness were measured post-process. The results demonstrated that precise control over cumulative sputtering time yielded well-defined patterns with expected average etching depths and surface roughness. This confirms the PIB technique’s potential for precise atomic depth image transfer and its suitability for industrial automation, offering a significant advancement in microfabrication technology.