A method and system for compensating for motion artefacts in Optical Coherence Tomography is provided. A B-scan set includes a plurality of B-scan images acquired at at least a position corresponding to a target position of a fundus of an eye. The plurality of B-scans within the B-scan set are aligned using a first alignment process and a second alignment process, where the second alignment process is performed on the B-scan images within the B-scan set aligned by the first alignment process. The first alignment process aligns the B-scan images within the B-scan set at a first resolution in at least an axial direction, and the second alignment process aligns the B-scan images within the B-scan set aligned in the first alignment process at a second resolution having a higher resolution than the first resolution in at least the axial direction.
