This disclosure relates to the field of Optical Coherence Tomography (OCT). This disclosure particularly relates to an OCT system having a configuration that uses a phase sensitive B-scan registration method. In this disclosure, an OCT system may have a configuration that scans a physical object, acquires OCT signals to form B-scans, uses these B-scans to determine an optimal shift in an axial direction by using total phase error between B-scans, and align B-scans, thereby minimizing effects of motion that may occur during scanning of the physical object.