To process micro-structured surface optical elements without surface damage and subsurface damage in higher efficiency, a numerical control system for Atmospheric Pressure Plasma Processing (APPP) was established. The design of a system platform, APPP process characteristics and numerical control process were investigated. First, according to the principle and requirements of the APPP, the numerical control system composition was presented. Then, by taking the processing of fused silica by He/SF6/O2 as an example, the controllability of the process as well as multi-parameter process characteristics were explored using the plasma torch with a needle electrode, and the removal function under this condition was fitted. Finally, the entire realization process of the numerical control machining for the APPP was proposed. Experimental results indicate that the sine structure with an amplitude of 150 nm and wavelength of 6 mm can be processed on a flat fused silica surface by this system, which verifies the feasibility of the numerical control system and achieves the deterministic processing of complex optical surfaces.