Optics with free form surface can be achieve special imaging effects and reduce component amounts in optical systems. However, it is difficulty to fabricate high accuracy, damage-free optical surface with free form surfaces by conventional method. Atmospheric plasma machining is a non-contact chemical processing method which can fabricate optics without damaged layer. Numerical controlled atmospheric pressure plasma machining (NC-APPM) method is proposed to machine optical free form surfaces. A new atmospheric pressure plasma jet generator was designed to get Gaussian rotational symmetry removal spot and the spot maximum diameter is 1.5mm. Base on dwelling time algorithm, a sinusoidal wave structure, the pitch 2mm and the amplitude 500 nm, is fabricated on a pre-polished flat silica quartz surface using three-axis numerically controlled machine made by ourselves. The result shows that the amplitude error is 59 nm compare to the expectation value surfaces using numerical controlled atmospheric plasma machining method.