EDM is the manufacturing process that uses the thermal energy to machine electrically conductive part. Despite a lot of research has been conducted for decades, the best aspect ratio of the micro hole using micro-EDM has not been over 30, yet. In the present study, new fabrication scheme was introduced to increase the aspect ratio of micro hole dramatically. Micro holes with less than 10 aspect ratio were aligned and welded together to manufacture a micro hole with extreme aspect ratio. Alignment of the micro hole with over 380 aspect ratio was conducted by the home-made apparatus installed with microscope and laser beam. The micro hole with extreme aspect ratio was used to shape pencil beam from proton beam generated from MC-50 cyclotron. The pencil beam was utilized to machine test specimen whose result was compared with GEANT4 computer simulation. It was shown that the experimental and simulation result were closer as the aspect ratio of the micro hole was bigger.