A shape identification program causes a computer to execute a process including: acquiring a third shape dataset and a fourth shape dataset, respectively generated by changing sizes of a first shape dataset and a second shape dataset in each of directions of a plurality of coordinate axes according to a specific rule; and generating a first plurality of images and a second plurality of images by capturing the third shape dataset and the fourth shape dataset, respectively, from both directions of the respective plurality of coordinate axes. The process further includes identifying a second portion in the second shape dataset corresponding to a first portion in the first shape dataset by aligning orientations of the first shape dataset and the second shape dataset based on a result of comparison between the first plurality of images and the second plurality of images.