E-Beam micro-hole drilling features high productivity of 2,000 holes per second and a high aspect ratio of 10 (depth/diameter). It can be used for the fabrication of nozzles and filters that require several holes. The hole-formation mechanism comprises 1) melting the sample by the energy exchange of e-beam and 2) removing the molten sample by the explosion of the backing material. Accordingly, hole-formation mechanism studies have focused on the effectiveness of backing material and the workpiece’s melting characteristic. This study investigated the melting depth characteristics depending on the beam current and exposure time that determines the E-Beam dose. The experiments were conducted without using the backing materials with an aim to investigate the melting characteristic of the workpiece itself. The results showed that the increase in the exposure current led to an improvement in the melting depth. The results were verified based on the comparison with the results of the process involving the backing material.