This study presents an investigation into the drilling of a deep microholes with the depth of 320 μm in tool steel SKD61 by the Micro-EDM process. The electrode with the diameter of 26 μm is machined by the method of wire electrodischarge grinding (WEDG). Optical microscopy, scanning electron microscopy, and confocal laser scanning microscopy techniques are used to determine the influence of the process parameters upon hole enlargement, electrode wear rate, material removal rate, wear ratio, and the observed surface topography. The results of the study reveal the optimum parameter settings for the Micro-EDM machining of a high aspect ratio microhole are as follows: (1) a pulse voltage between 60 and 100 V, (2) a capacitance between 80 pF and 220 pF. Finally when the depth exceeds 200 μm, the shape of the micro hole almost becomes tapered due to the corner wear of the electrode and the secondary discharge along the side of the hole.