A method and system to map density and temperature of a chip, in situ, is disclosed. The method includes measuring a propagation time that a mechanical propagation wave (100) travels along at least one predefined path (12, 14) in a substrate (10). The method further includes calculating an average substrate density and temperature along the at least one predefined path as a function of the propagation time and distance. The method further includes determining a defect or unauthorized modification (18) in the substrate based on the average substrate density being different than a baseline substrate density.