1. A three-dimensional shape 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; a restoration unit configured to restore first three-dimensional shape data based on the first tomographic image group and second three-dimensional shape data based on the second tomographic image group; an estimation unit configured to estimate an accuracy value of the first and second three-dimensional shape data at a plurality of positions; and a combination unit configured to combine the first and second three-dimensional shape data into one piece of three-dimensional shape data based on the estimated accuracy values of the first and second three-dimensional shape data estimated by the estimation unit at the plurality of positions.