Orthodontic practitioners are eager to incorporate 3D technologies to better manage treatment planning. CBCT has created a turning point in the discipline because it allows practitioners to achieve a better understanding of patients’ anatomy and thus establish a more customised and precise approach, especially in cases of transverse expansion, anteroposterior torque and translation movements. Clear aligner treatment and the use of CBCT offer countless advantages, such as preservation of patients’ periodontal health, and this seems to herald a more promising future. The present article develops arguments in favour of the implementation of a biodigital protocol with the purpose of fully preserving the supporting tissues of each tooth and integrating 3D digital technologies for diagnosis and planning in all clear aligner treatments. Thus, the authors present a clinical case treated using the abovementioned protocol.