Low energy-short pulsed electric discharge coupled with precise movement of circular electrode in micro-electrical discharge-milling (μ-EDM-milling) enables generation of three-dimensional (3D) cavities in the order of few tens of microns. Use of unshaped rotating electrode alters the spark discharge pattern that is primarily driven by the shape and size of the cavities being machined. In this paper, effects of five different cavities: circular, triangular, square, channel, and cross channel (square pillars) on the machining performance have been studied. These cavities having a nominal dimension of 1000 μm were machined on steel sample using 200 μm tungsten carbide electrode. The machining performance has been evaluated by analyzing dimensional accuracy, surface integrity, profile error, and formation of recast layers. The results highlight significant shape effect on machining performance in μ-EDM-milling. Circular holes machined by die sinking (tool advancement in Z-axis) are found to be more accurate, and square shaped pillars machined in two settings by generating cross channels at 90 deg have poor dimensional control. On the other hand, triangular cavities have the highest surface finish and profile uniformity compared to other shapes. The microscopic study in scanning electron microscopy (SEM) reveals significant variations in globule formation, recast layer deposition, flow of eroded molten metal, and final shape of cavities, which are found to be dependent of tool rotation.