Micro-machining by mechanical machine tool, or micro mechanical machining, is an emerging fabrication technology that broadens applicable material ranges including metals and plastics. One of the problems in this micro machining, however, is relatively large run-out which is comparable to the diameter of tools. A series of experiments were conducted to identify Total Indicator Reading (TIR) and dynamic run-out of micro-machining on aluminum workpieces. Results presented in this paper indicate the ratio of run-out to tool diameter ranged between 2.2% and 10%. To compensate for the run-out in the design stage of micro features, a Java-based Design for Manufacturing (DFM) tool was developed. This tool can assist designers to design micro channels accurately considering the effect of run-out. Furthermore, the feasibility of micro-injection molding was examined with micro-machined channels. Micro-molded parts were made from ABS plastic showing negligible shrinkage from the molding process.