A method for motion correcting molecular breast imaging (MBI) images includes obtaining a plurality of two-dimensional (2D) images of a breast using a MBI system, selecting a reference image from the plurality of 2D images, selecting a feature of interest in the reference image, determining a location of the feature of interest in the reference image, calculating a correction value based on a difference in the location of the feature of interest in the reference image and a location of the feature of interest in a plurality of non-reference images, and aligning the non-reference 2D images with the reference image based on the calculated correction value.