Micro machining by wire electrical discharge machining (WEDM) has become prosperous owing to its ability to machine conductive, exotic and high strength and temperature resistive (HSTR) materials with the scope of generating intricate shapes and profiles. In order to achieve the very high accuracy micro machining, one of the key factors is the preparation before actual machining. According to the authors' experiences and studies in micro machining by WEDM, for the first time, this paper introduces the preparation process for WEDM in micro machining. From the gauge setup, wire alignment adjustment, working coordinate setup to calibration method for rotational axis, the preparation process has been studied and introduced in detail, which forms the solid basis for high accuracy micro machining by WEDM. Experimental results show the accurate geometrical features can be fabricated based on the proposed preparation process.