Micro Electric Discharge Machining is mostly used micromachining technique for manufacturing of micro holes and mini cavities. It is a thermal material removal process achieved by application of recursive electrical sparks between two conductive materials immersed in dielectric liquid. There are many electrical and technological parameters, which are effective in the machining characteristics and machined material surface integrity. In this study, effects of pulse energy on characteristics of surface damage in micro electric discharge machining of micro holes are investigated. To observe the influences of investigated pulse forms, a series of micro-holes were machined and cut from cross sections for metallurgical examinations. Unconventional etching agents were applied to examine the metallurgical transformations using optical and scanning electron microscopy. It was observed that heat-damaged segment is composed of three distinctive layers, have relatively high thicknesses (0.2 to 10 μm) when compared with the size of the micro holes and varies noticeably with respect to drilling dept. Different morphological structures and deformations in the subsurface of micro-hole walls at several sections were illustrated. Finally, analyzed machining parameters and variation of hat damaged layer thicknesses were discussed in terms of drilling depth.