By taking a 3-DOF translational milling machine as an example, this paper investigates the kinematic calibration of PKM systems with fewer than 6-DOF. The error mapping function is formulated in such a way that the geometric errors affecting the compensatable and uncompensatable pose errors can be separated. Based upon the previous investigation, a hierarchical approach to the geometric error identification is proposed. The compensation strategy is developed which is particularly suitable for the PKM systems with translational moving capability. The experiment has been carried out to verify the effectiveness of the proposed approach and the results show that the accuracy can be significantly improved.