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Eddy-current testing (ECT) is widely used in inspection of multilayer aircraft skin structures for the detection of cracks under fasteners (CUF). Detection of deep hidden CUF poses a major challenge in traditional ECT techniques largely because the weak eddy-current signal due to a subsurface crack is dominated by the strong signal from the aluminum or steel fastener. Giant magnetoresistive (GMR) sensors are finding increasing applications in directly measuring weak magnetic fields associated with induced eddy currents. The measured flux image at a fastener site is in general symmetric and an asymmetry is introduced by the presence of a subsurface crack, which is used for defect detection. This paper presents novel methods that employ the resident phase information, for improving detection probability of GMR signal analysis. Using computational model, the effectiveness of the proposed methods for enhancing detection of CUF is investigated. Results demonstrating the potential of these techniques for detection of second layer CUF are presented.