Background/Objectives: Clear aligner therapy has become a mainstream alternative to fixed orthodontics due to its versatility. However, the variability in thermoforming and the limited validation of digital workflows remain major barriers to reproducibility and predictability. Methods: This study addresses that gap by presenting a proof-of-concept digital workflow for clear aligner manufacturing by integrating additive manufacturing (AM), thermoforming simulation, and finite element analysis (FEA). Dental models were 3D-printed and thermoformed under clinically relevant pressures (400 kPa positive and −90 kPa negative). Results and Discussion: Geometric accuracy was quantified using CloudCompare v2.13.0, showing that positive-pressure thermoforming reduced maximum deviations from 1.06 mm to 0.4 mm, with all deviations exceeding the expanded measurement uncertainty. Thickness simulations of PETG sheets (0.5 and 0.75 mm) showed good agreement with experimental values across seven validation points, with errors <10% and overlapping 95% confidence intervals. Stress analysis indicated that force transmission was localized at the aligner–attachment interface, consistent with expected orthodontic mechanics. Conclusions: By quantifying accuracy and mechanical behavior through numerical and experimental validation, this framework demonstrates how controlled thermoforming and simulation-guided design can enhance aligner consistency, reduce adjustments, and improve treatment predictability.