We report a precise, simple, and accessible method of mathematically measuring and modeling the three-dimensional (3D) geometry of semicircular canals (SCCs) in living humans. Knowledge of this geometry helps understand the development and physiology of SCC stimulation. We developed a framework of robust techniques that automatically and accurately reconstruct SCC geometry from computed tomography (CT) images and are directly validated using micro-CT as ground truth. This framework measures the 3D centroid paths of the bony SCCs allowing direct comparison and analysis between ears within and between subjects. An average set of SCC morphology is calculated from 34 human ears, within which other geometrical attributes such as nonplanarity, radius of curvature, and inter-SCC angle are examined, with a focus on physiological implications. These measurements have also been used to critically evaluate plane fitting techniques that reconcile many of the discrepancies in current SCC plane studies. Finally, we mathematically model SCC geometry using Fourier series equations. This work has the potential to reinterpret physiology and pathophysiology in terms of real individual 3D morphology.