In a large-area electron beam (EB) irradiation method developed recently, high energy EB can be obtained without focusing the beam, and large-area EB with almost uniform energy density distribution of 60mm in diameter can be used for instantly melting and evaporating metal surface. Then, the surface smoothing and surface modification of metal molds made of steel, cemented carbide and ceramics can be performed efficiently. When the large-area EB is irradiated to a sharp edge, the material removal remarkably progresses at the edge due to the heat accumulation and EB concentration there, which leads to the edge rounding. Our previous study clarified that micro-deburring was also possible by using this phenomenon. Moreover, this method would be effective for removal of discontinuous micro burrs generated by thermal machining processes, such as EDM and laser cutting. In this study, the possibility to completely remove micro burrs generated in EDM was experimentally investigated. The difference in micro-deburring characteristics with the type of workpiece material was also investigated. As a result, the EDM micro burrs with a height of about up to 50μm could be completely removed by this method. Furthermore, it was made clear that the magnetic property of workpiece materials greatly influenced the deburring characteristics, and the thermal property such as melting point and thermal conductivity also did.