Estimation of defect depth and size is an important problem in the domain of Nondestructive Testing in order to perform corrective repairs. The problem of defect depth estimation using Infrared Thermography has been previously studied using 1D heat conduction models. Unfortunately, 1D heat conduction based models are generally inadequate in predicting heat flow around finite-sized defects, especially in composite structures. In this study, a novel approach based on 3D heat conduction is proposed to model the heat flow interaction with the defect in quasi-isotropic composite materials. The modeling process involved coordinate transformations to reduce the anisotropic heat conduction problem to the isotropic domain, followed by separation of variables to solve the partial differential equation of the heat conduction. The validity of the model is established using Pulsed Thermography experiments performed on a composite panel containing rectangular flat-bottom holes of different sizes, present at different depths.