Lock-In Thermography is an established nondestructive method for analyzing failures in microelectronic devices. In recent years, a major improvement made it possible to acquire time-resolved temperature responses of weak thermal spots, greatly enhancing defect localization in 3D stacked architectures. One limitation, however, is in the method used to determine defect depth, which is based on the numerical estimation of the delay between excitation and thermal response inferred from the value of the lock-in phase. In structures where the region between the origin of the defect and sample surface is partially or fully transparent to infrared signals, interference between radiated and conducted signal components largely falsifies the phase value on which the classical depth estimation relies. In the present study, blind source separation based on independent component analysis was successfully used to separate interfering signal components arising from direct thermal radiation and conduction, resulting in a precise estimation of the defect depth.