A series of digital frequency filters (DFFs) were designed to screen diverse noises and the spectrographic analysis was conducted to isolate complex boundary reflection, which obscures the damage-induced signals. The scale-averaged wavelet power (SAP) technique was applied to enhance the measurement accuracy of Time of Flight (TOF). As an example, the propagation characteristics of elastic wave in a structural beam of square cross-section were analyzed using such an approach and verified experimentally and numerically, with the consideration of the complicated wave scatter caused by the non-ignorable section dimensions.