The paper treats the issue of embedding the traceable length metrology into technological process by performing precise dynamic measurements of line scale in its manufacture line. It addresses the error-related problems specific to line scale calibration in dynamic mode of operation that are caused primarily by dynamic loads. Introducing the dynamic regime of calibration leads to the dynamic calibration error originating due to vibration sources in the structure. This uncertainty contribution should be considered and implicated in the total uncertainty budget. A new 3D finite element model was 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. Both the dynamically induced deviations and current capabilities to carry out line scale calibrations were examined experimentally. The experiments were conducted on the interferometer-controlled comparator setup with a moving microscope that was further developed to reduce the calibration repeatability error.