A system and method to measure, with increased precision, the transit time position(s) of pulses in a time domain data. An example data set would be the transit time of pulses in Time-Domain Terahertz (TD-THz) data. The precision of the pulse timing directly affects the precision of determined sample properties measurements (e.g., thickness). Additionally, an internal calibration etalon structure and algorithm method provides for continuous system precision/accuracy check method to increase sample measurement integrity. The etalon structure can improve the precision of sample property measurements (e.g., absolute thickness). Various hardware and system implementations of the above are described.