This article demystifies the operational workflow of AI-driven clear aligner design software, moving beyond the final patient-facing animation to examine four core computational stages. First, prescription input captures the clinical directive—including extraction protocols, expansion strategies, IPR tolerance, and anchorage requirements. Second, model preprocessing performs attachment removal, mesh repair, and occlusal plane orientation to prevent error propagation through subsequent steps. Third, segmentation and target setup employ AI to identify tooth boundaries, arch perimeter discrepancies, and baseline target occlusions, though target position validity remains fundamentally dependent on clinical experience. Fourth, staging and attachment optimization calculate incremental tooth movements and recommend biomechanical control auxiliaries. The article argues that what separates effective AI from superficial automation is not computational speed but clinical logic, dataset depth, and quality control architecture. It highlights the critical distinction between crown alignment and anatomically sound treatment, emphasizing that without post-training on large, CBCT-enriched, clinically validated datasets, AI systems default to superficial tooth straightening rather than biomechanically informed movement—resulting in unnecessary refinements and restarts, particularly in moderate and complex malocclusions.