Numerical simulation of long-term orthodontic tooth movement based on Finite Element Analysis (FEA) could help clinicians to plan more efficient and mechanically sound treatments. However, most of FEA studies assume idealized loading conditions and lack experimental calibration or validation. The goal of this paper is to propose a novel clinical protocol to accurately track orthodontic tooth displacement in three-dimensions (3D) and provide 3D models that may support FEA. Our protocol uses an initial cone beam computed tomography (CBCT) scan and several intra-oral scans (IOS) to generate 3D models of the maxillary bone and teeth ready for use in FEA. The protocol was applied to monitor the canine retraction of a patient during seven months. A second CBCT scan was performed at the end of the study for validation purposes. In order to ease FEA, a frictionless and statically determinate lingual device for maxillary canine retraction was designed. Numerical simulations were set up using the 3D models provided by our protocol to show the relevance of our proposal. Comparison of numerical and clinical results highlights the suitability of this protocol to support patient-specific FEA.