Acquired adult flatfoot is a frequent deformity which implies multiple, complex and combined 3D modifications of the foot skeletal structure. The difficult thorough evaluation of the degree of severity pre-op and the corresponding assessment post-op can now be overcome by cone-beam (CBCT) technology, which can provide access to the 3D skeletal structure in weight-bearing. This study aims to report flatfoot deformities originally in 3D and in weight-bearing, with measurements taken using two different bone segmentation techniques. 21 such patients, with indication for surgical corrections, underwent CBCT (Carestream, US) while standing on one leg. From these scans, 3D models of each bone of the foot were reconstructed by using two different state-of-the-art segmentation tools: a semi-automatic (Mimics Innovation Suite, Materialise, Belgium), and an automatic (Bonelogic Ortho Foot and Ankle, Disior, Finland). From both reconstructed models, Principal Component Analysis was used to define anatomical reference frames, and original foot and ankle angles and other parameters were calculated mostly based on the longitudinal axis of the bones, in anatomical plane projections and in 3D. Both bone model reconstructions revealed a considerable valgus of the calcareous, plantarflexion and internal rotation of the talus, and typical Meary's angles in the lateral and transverse plane projections. The mean difference from these angles between semi-automatic and automatic segmentations was larger than 3.5 degrees for only 3 of the 32 measurements, and a large number of these differences were not statistically significant. CBCT and the present techniques for bone shape reconstruction finally provide a novel and valuable 3D assessment of complex foot deformities in weight-bearing, eliminating previous limitations associated to unloaded feet and bidimensional measures. Corresponding measurements on the bone models from the two segmentation tools compared well. Other more representative measurements can be defined in the future using CBCT and these techniques.