Micro-burrs deteriorate machined surface quality and cause damage to the contact surfaces of parts; therefore, they should be removed through the deburring process. However, micro-burrs are not easy to remove, making it necessary to suppress the generation of micro-burrs by optimizing the machining process and advanced methodology. In this paper, an effective machining method to suppress micro- burrs and the relationship between burr size and cutting signals were investigated in the micro-milling process. In order to derive a machining method to minimize the generation of micro-burrs, a micro-channel was machined by a total of four machining methods, the size of the exit burr and top burr were measured, and an effective machining method was selected in based on the analysis of micro-burr generation. The relationship between the micro-burrs and the AE signals was determined by an analysis of cutting signals and micro-burr shape.