This paper presents a novel process using micro-electro-discharge- machining (micro-EDM) combined with ultrasonic vibration by a helical micro-tool electrode to drill and finish micro-holes. During the machining processes, a micro-tool is directly fabricated by wire electro-discharge grinding (WEDG) using micro-EDM combined with various methods for machining the micro-hole and by ultrasonic vibration to finish the hole wall. In this work, circular micro-holes are machined in a high nickel alloy by cylindrical and helical electrodes. Using a helical micro-tool electrode for micro-EDM combined with ultrasonic vibration (HE-MEDM-UV) can substantially reduce the EDM gap, taper and machining time for deep micro-hole drilling. In addition, using a helical micro-tool with micro ultrasonic vibration finishing (HE-MUVF), good surface quality and less taper of the hole wall can be obtained by applying a suitable electrode step variation, rotational speed and ultrasonic amplitude with a machining time of approximately 25 min. According to scanning electron microscopy (SEM) micrographs and atomic force microscopy (AFM) measurement, HE-MUVF can indeed improve the surface roughness from 1.345 νm Rmax before finishing to 0.58 νm Rmax after HE-MUVF. This result demonstrates that using HE-MEDM-UV combined with MUVF can yield micro-holes of precise shape and smooth surface.