In this paper a three-sided pyramidal tip was driven in a circular trajectory to perform micro-machining process. The circular trajectory was achieved by rotating the tip around a center point. Because of the asymmetry of the three-sided pyramidal tip, machining micro channels along different feeding directions would cause different cutting tracks, which influences the finish of channel sides. It was found that the variations of cutting rake angle and uncut chip thickness in each revolution mainly affected the burr formation. By studying effects of tip edge radius and tip geometry on machining process, a channel with slight burr at two sides was obtained. Using the optimized machining method and coordinating with feed motion of the work stage, perfect three-dimensional structures with well-finishing edges were obtained on aluminum alloy and polymethylmethacrylate (PMMA) surfaces. The dimension of fabricated 3D structures can be controlled in three dimensional directions, ranging from ten microns to several hundred microns.