PROBLEM TO BE SOLVED: To realize the restoration of high picture quality three-dimensional data with small distortion.SOLUTION: A three-dimensional data processing apparatus includes: a data input unit 121 for receiving input of data of a first tomographic image group composed of a plurality of tomographic images, and data of a second tomographic image group composed of a plurality of tomographic images obtained by overlapping at least a portion of the first tomographic image group on an imaging area a thee-dimensional shape restoration unit for restoring first three-dimensional shape data from the first tomographic image group, and restoring second three-dimensional shape data from the second tomographic image group a probability estimation unit 123 for estimating the probabilities of a plurality of positions in each three-dimensional shape data of the first three-dimensional shape data and the second three-dimensional shape data and a three-dimensional shape synthesis unit 124 for performing synthetic processing for synthesizing the first three-dimensional shape data and the second three-dimensional shape data to one piece of three-dimensional shape data on the basis of estimation values of the probabilities of the plurality of positions in each estimated three-dimensional shape data.
