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(1) Background: Facial scanners are used in different fields of dentistry to digitalize the soft tissues of the patient’s face. The development of technology has allowed the patient to have a 3-dimensional virtual representation, facilitating facial integration in the diagnosis and treatment plan. However, the accuracy of the facial scanner and the obtaining of better results with respect to the manual or two-dimensional (2D) method are questionable. The objective of this clinical trial was to evaluate the usefulness and accuracy of the 3D method (a dual-structured light facial scanner) and compare it with the 2D method (photography) to obtain facial analysis in the maximum intercuspation position and smile position. (2) Methods: A total of 60 participants were included, and nine facial landmarks and five interlandmarks distances were determined by two independent calibrated operators for each participant. All measurements were made using three methods: the manual method (manual measurement), the 2D method (photography), and the 3D method (facial scanner). All clinical and lighting conditions, as well as the specific parameters of each method, were standardized and controlled. The facial interlandmark distances were made by using a digital caliper, a 2D software program (Adobe Photoshop, version 21.0.2), and a 3D software program (Meshlab, version 2020.12), respectively. The data were analyzed by SPSS statistical software. The Kolmogorov–Smirnov test revealed that trueness and precision values were normally distributed (p > 0.05), so a Student’s t-test was employed. (3) Results: Statistically significant differences (p ≤ 0.01) were observed in all interlandmark measurements in the 2D group (photography) to compare with the manual group. The 2D method obtained a mean accuracy value of 2.09 (±3.38) and 2.494 (±3.67) in maximum intercuspation and smile, respectively. On the other hand, the 3D method (facial scanner) obtained a mean accuracy value of 0.61 (±1.65) and 0.28 (±2.03) in maximum intercuspation and smile, respectively. There were no statistically significant differences with the manual method. (4) Conclusions: The employed technique demonstrated that it influences the accuracy of facial records. The 3D method reported acceptable accuracy values, while the 2D method showed discrepancies over the clinically acceptable limits.