The traditional CNC system is established on conventional machine tool mainly using ball screws. This could not suitable for micro mechanical machining with linear motor which could provide high speed, high precision, fast response and zero backlash. In this paper, a 3-axis micro milling machine tool with an open CNC system has been developed based on motion controller and linear motors. Considering the requirements of micro milling several special functions just like micro cutting tool setting are provided in exploited control software. The system dynamic characteristics are evaluated through experiments with servo parameters adjustments. In the following machining experiments, the whole system is proved economically and effectively.