Clear aligner therapy (CAT) has progressed from a niche adjunct to a dominant modality in contemporary orthodontics. This manuscript frames that trajectory as a sequence of scientific-revolution stages—pre‑science, normal science, model drift, model crisis, and model revolution—to clarify how conceptual and technological shifts have reshaped clinical practice and research priorities. We synthesize developments in digital workflows (intraoral scanning, CBCT integration), AI‑driven treatment staging, and personalized biomechanics, and we evaluate methodological limitations in current CAT studies that hinder reliable data interpretation. Key gaps include inconsistent outcome definitions, limited external validity of small or vendor‑sponsored trials, insufficient biomechanical and materials characterization, and sparse patient‑centered endpoints. These limitations inflate uncertainty around dose–response relationships, material behaviour under clinical conditions, and the real‑world effectiveness of algorithmic staging tools. To enhance evidence quality and patient outcomes, we propose stronger research designs—prospective, adequately powered, multi-center trials; standardized outcome metrics; preregistration and transparent data sharing; robust biomechanical and materials testing; and integrated health‑services research to assess access, costs, and patient preferences. We also advocate development and validation of AI‑assisted decision‑support tools within rigorous clinical frameworks. Multidisciplinary, methodologically rigorous research and consensus on outcomes are essential to translate digital innovations in CAT into predictable, patient‑centred care. Implementing improved study designs and transparent practices will better define effective protocols, guide policy, and ultimately improve clinical outcomes for patients receiving clear aligner therapy.
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