The paper addresses the error-related problems specific to line scale calibration in dynamic mode of operation that are caused primarily by geometrical and thermal deviations of the calibration system components. A new 3D finite element model has been developed in order to both investigate thermo-mechanical processes in the comparator structure and evaluate possible temperature influence on geometrical dimensions of the line scale. An interferometer-controlled comparator setup with a moving microscope has been designed to evaluate the performance of the long scale calibration process.