Micro end-milling is a highly-efficient machining process and can be used to machine high hardness metal mold directly; therefore, it is applied to the machining of micro channel structures. There are conventional methods to fabricate the micro channels such as lithography, etching and laser processing; however, they have some demerits of high cost, limitation of materials and complex processes. Machining molds with micro channel structures for mixers using micro end-mills have been studied. According to recent study, ultra micro end-milling technology is required in order to improve the efficiency of mixers because the micro structures are double-layered channels. Tool breakage and micro burrs are issues due to diameter of the micro end-mill getting smaller. Machining characteristics using ф 50 and 30 µm end-mill on 64 brass and STAVAX were studied in order to machine the micro complex channels. Tool stability and burrs were studied through analysis of the cutting force and cutting conditions. A micro-mixer mold with double-layered channel structures was machined.