Calibration is crucial for hexapods with high-accuracy positioning capability. Many of these calibration procedures require measurement of hexapod's platform pose (position and orientation) at constant temperature. Consequently, thermal deflection of the hexapod's platform during pose measurements impacts the accuracy of calibrated parameters. This paper presents a method to eliminate the impact of thermal deflection of hexapods on their pose measurement. In this method, a reference pose is measured before each measurement of any particular pose. The measurements of reference pose are used to estimate thermal deflection of hexapod's legs. This is in turn used to estimate and correct the resulting pose error at the particular pose to be measured. The advantage of using the proposed method is demonstrated experimentally by means of pose measurements of a high-precision hexapod using a CMM.