The dies or molds used for the fabrication of micro products usually are made of ultra-hard materials such as tungsten carbide or silicon carbide and have sophisticated three-dimensional geometries. Such kind of dies or molds can only be fabricated by milling operations instead of grinding processes with ultra-hard milling tools made of PCD or CBN. Electrical discharge machining (EDM) is a good choice for the fabrication of such ultra-hard tools. In this paper, a function analysis and design of a six-axis Wire EDM (WEDM) machine is introduced. Based on the typical micro/nano cutting tool geometry features, a mathematical model between the cutting tool and the electrode wire is built. Then, the mathematical model is analyzed and it turns out that six axes are needed for cutting such complicated tool geometries. According to the WEDM features, first the axes are allocated to the workpiece side and the electrode wire side. The workpiece is assigned three linear motions and one rotary motion around its center line and the wire has two rotary motions. Second, the axis sequences are defined. At last, the best concept of the mechanical structure for the six-axis WEDM machine is selected.