Physical phenomena in thin multi-layer carbon fiber reinforced polymer (CFRP) materials with defects are not always easily definable through experimental observations of thermography nondestructive testing (TNDT). The current research focuses on the transient heat distribution of the finite element model of a seven-layer CFRP plate with embedded defects. The simulated heating load is applied at the back surface of the three-dimensional FE model such that the thermal analysis is carried out to characterize the temperature profiles along various observation lines across the front surface. The sizes of the embedded defects at different depths are estimated by the full width half maximum (FWHM) method. The simulation results are verified experimentally against a CFRP specimen based on the same model design using active thermography. The defect sizes can be determined successfully by FWHM only if the surface temperature profiles are pre-processed by the data averaging technique.