Surgical splints are widely used in orthognathic surgery. The fitting of a surgical splint affects the success of the surgery. Stereolithography (STL), the method used to achieve accurate and reliable input files, is important for the manufacturing process of the surgical splint. Nowadays, data acquisition can be performed with the aid of an intraoral scanner (IOS) or impression materials. This in vitro study aimed to compare the trueness and precision of IOS (TRIOS3®, 3Shape, Copenhagen, Denmark) and alginate impression (Kromopan®, Lascod, Florence, Italy) in a full-arch dental model with/without orthodontic brackets. Custom complete arch models were fabricated with a refractive index similar to that of tooth structure. A TRIOS3® intraoral scanner (3Shape, Copenhagen, Denmark) and an alginate impression were used to duplicate the custom model without orthodontic brackets for complete arch scenarios (both upper and lower arches), n = 5. Subsequently, orthodontic brackets (Ormco®, Glendora, CA, USA) were attached to the custom model and the TRIOS® intraoral scanner and alginate impression were used again. Analysis was performed using 3-dimensional (3D) metrology software (GOM inspect®, GOM GmbH, Braunschweig, Germany) to measure surface deviations between the STL files from the custom model to evaluate and compare their trueness and precision. All data were entered into Microsoft Excel and then transferred to SPSS (Statistical Package for the Social Sciences). The average surface deviations were compared between the TRIOS3® intraoral scanner and the alginate impression using a repeated measures ANOVA (Analysis of Variance) with adjustment for multiple comparisons using Bonferroni’s correction. There were no significant differences in trueness and precision between TRIOS3® and alginate impression in full arch models with and without orthodontic brackets. Moreover, the accuracy of all groups was less than 100 microns, which was acceptable. Further in vivo studies are required to confirm these results.