1. A three-dimensional data processing apparatus comprising: a data input unit configured to input data of a first tomographic image group including a plurality of tomographic images and data of a second tomographic image group including a plurality of tomographic images, wherein at least a part of an image capturing area of the second tomographic image group is overlapped with at least a part of an image capturing area of the first tomographic image group; an estimation unit configured to estimate accuracy values at each of a plurality of points related to the first tomographic image group and the second tomographic image group, based on a first direction of at least a part of the tomographic images included in the first tomographic image group and a second direction of at least a part of the tomographic images included in the second tomographic image group, wherein the first direction differs from the second direction; and a combination unit configured to combine the first tomographic image group and the second tomographic image group into one piece of three-dimensional data based on the accuracy values estimated by the estimation unit.