This study aimed to gain an in-depth understanding of the features of AFM micro probe nanomachining. With the aid of the orthogonal test analysis and synthesis method of point rating, factors of influencing the cutting process: the perpendicular load, the feed amount and the cutting speed, were analyzed. The study revealed that the feed amount and the perpendicular load had greater effect on the surface quality and machining efficiency than the cutting speed. The results were also compared with the conventional ultra-precision machining. The optimal machining parameters suitable for two application fields were achieved. This method is a novel and feasible method to perform the nanomachining.