Micro/nano milling tools are usually made of ultra hard materials. Wire EDM (electrical discharge machining) may be the best choice to fabricate these tools conveniently and efficiently. For micro/nano milling tools with complicated three-dimensional (3D) geometries, manually programming method is not applicable. The CAM (computer-aided manufacturing) systems existing in the market don't take the special WEDM (Wire EDM) processes for micro/nano milling tools into consideration. In order to generate the NC programs automatically for the multi-axis WEDM machine to fabricate micro/nano milling tools, a computer assistant system, also called the CAM system, is developed in this paper. The CAM system takes the special WEDM processes into consideration for the fabrication of micro/nano milling tools. First, based on the interfaces and the databases of the CAM system, geometries of micro/nano milling tools, machining conditions for different portions of the tools, WEDM machine tool specifications and controller properties are defined. Second, the manually input tool geometries are verified and WL (wire location) data are generated and verified. Third, simultaneously maximum six-axis CNC programs are generated automatically for the specific micro/nano milling tool. Key techniques for the development of the CAM system are introduced in the paper and micro/nano milling tool fabrication experiment done in this paper shows the efficiency and accuracy of the CNC program generated by the developed CAM system.