To test the impact of FFF filaments, printing parameters, thermoforming foils, repeated thermoforming cycles, and type of jaw on the dimensional stability of FFF models for aligners and to compare them with plaster models, FFF models (maxilla, n = 48; mandible, n = 48) from two filaments (SIMPLEX aligner and Renfert PLA HT, both Renfert GmbH) were fabricated using four printing parameters (one, two, or three loops; four loops acted as the default) and conventional plaster models (n = 12) based on a young, female dentition. All models were thermoformed under pressure three times in total using two different thermoforming foils, namely 0.75 mm × 125 mm Ø aligner foil (CA Pro+ Clear Aligner, Scheu Dental) and 1.0 mm × 125 mm Ø Duran foil (Duran+, Scheu Dental). Aligner foil was heated at 220 °C for 25 s and Duran foil at 220 °C for 30 s. All models were scanned after fabrication as well as after each thermoforming cycle. The obtained STL datasets were analyzed using the local best-fit method (GOM Inspect Pro, Carl Zeiss Metrology GmbH). Data were analyzed using a Kolmogorov–Smirnov-test, a one-way ANOVA with post-hoc Scheffé, and at-test (p< 0.05). The dimensional stability of the models was most strongly affected by the printing parameters (number of loops; ηp2= 0.768,p< 0.001) followed by the thermoforming foil used (ηp2= 0.663,p< 0.001) as well as the type of model (ηp2= 0.588,p< 0.001). In addition, various interactions showed an influence on the dimensional stability (ηp2= 0.041–0.386,p< 0.035). SIMPLEX maxillary models (default; four loops), thermoformed using aligner foil, showed higher deformation stability than did plaster models. These initial FFF models provide comparable precision to plaster models, but the dimensional stability of the FFF models, in contrast to that of plaster models, decreases with increasing numbers of thermoforming cycles.