Clinical management of foot pathology requires accurate and robust measurement of the anatomical angles. In order to measure a 3D angle, recent approaches have adopted a landmark-based local coordinate system to establish bone angles used in orthopedics. These measurement methods mainly assess the relative angle between bones using a representative axis derived from the morphological feature of the bone and therefore, the results can be affected by bone deformities. In this study, we propose a method of deriving a global frame-of-reference to acquire consistent direction of the foot by extracting the undersurface of the foot from the CT image data. The two lowest positions of the foot skin are identified from the surface to define the base plane, and the direction from the hallux to the fourth toe is defined together to construct the global coordinate system. We performed the experiment on 10 volumes of foot CT images of healthy subjects to verify that the proposed method provides reliable measurements. We measured 3D angles for talus-calcaneus and talus-navicular using facing articular surfaces of paired bones. The angle was reported in 3 projection angles based on both coordinate systems defined by proposed global frame-of-reference and by CT image planes (saggital, frontal, and transverse). The result shows that the quantified angle using the proposed method considerably reduced the standard deviation (SD) against the angle using the conventional projection planes, and it was also comparable with the measured angles obtained from local coordinate systems of the bones. Since our method is independent from any individual local shape of a bone, unlike the measurement method using the local coordinate system, it is suitable for inter-subject comparison studies.