Based on the prior work on the six degrees of freedom (6DOF) motion errors measurement system for linear axes, and for the different types of machine tools and different installation methods, this study used a ray tracing idea to establish the measurement models for two different measurement modes: (1) the measurement head is fixed and the target mirror moves and (2) the target mirror is fixed and the measurement head moves. Several experiments were performed on the same linear guide using two different measurement modes. The comparative experiments show that the two measurement modes and their corresponding measurement models are correct and effective. In the actual measurement process, it is therefore possible to select the corresponding measurement model according to the measurement mode. Furthermore, the correct motion error evaluation results can be obtained.