A new process of fabricating microstructures through micro electrochemical milling (micro EC milling) is proposed. The experiment equipment with a new type of ultra-short pulse supply was developed for micro EC milling. By controlling the movement track of simple micro tool electrode rotating at high speed on NC three-axis feed worktable, microstructures with high precision can be milled by micro-ECM under ultra-short pulse current. Micro EC milling can greatly improve the machining status in the tiny machining gap and thus make machining stable by simple rotary column electrode. The process of the NC generating micro-ECM integrating CAD/CAM technology is studied. G code for machining complex microstructures can be generated by the universal CAD/CAM of traditional milling based on UG software. Last, Microstructures with high precision were milled by this process, for example the micro trench with width of about 50μm.