The article treats the issue of embedding the traceable length metrology directly into technological process by performing precise dynamic measurements of line scale in real industrial environment. It addresses the error-related problems specific to line scale calibration in dynamic mode of operation that are caused primarily by static and dynamic loads as well as geometrical deviations of the calibration system components. Introducing the dynamic regime of calibration leads to the dynamic calibration error originating due to vibration sources in the structure. This term should be considered and implicated in the measurement uncertainty budget. A new 3D finite element model has been developed in order to both investigate the influence of dynamical excitations of a long stroke comparator structure and evaluate possible influence of vibrations on geometrical dimensions of the line scale. The experiments have been conducted on the new interferometer-controlled comparator setup with a moving microscope in order to evaluate the performance of the precision scale calibration process.