In machining of a microstructure on a free form surface, a five-axis ultra-precision machine tool has a great advantage in its flexibility and efficiency compared to a conventional machine tool. However, rotary axes in the five-axis machine tool are sensitive to position errors due to low rigidity. In addition, micro-tools, which are utilized in micro-machining, have low stiffness. The low rigidity and stiffness of the rotary axes and tool introduce geometric errors in machining. Therefore, the position and orientation errors of the rotary axes and the micro-tool must be identified and compensated. Many components contribute to uncertainty of the measurements which will inevitably reduce the reliability of the results. Therefore, it is necessary to analyze the uncertainty of each component. This paper proposed a method to comprehensively identify position-independent geometric errors (PIGEs) and force-induced errors (FIEs) of a system from the rotary axis on the machine to the micro-tool. A simple and practical error model to represent the tool position with respect to the angle of the rotary axis was built. Uncertainty was analyzed to validate the reliability of the proposed method. Cutting experiments were carried out on an AISI 1018 steel and an Al6061 workpiece, and the results were analyzed to verify the proposed model.