Intraoral three-dimensional scanning techniques could be used to improve dental practice, leading to an improved overall quality of the prosthetic devices and improved comfort for the patient. An accurate and precise intraoral scanner allows proper diagnosis, follow-up evaluation, and prosthesis application. The aim of this research is to evaluate the precision of an intraoral scanners (Medit i500, Medit Corp., Seoul, Korea), using open-source software in the digital workflow. The precision was compared through repetitions of the scanning process of the upper dental arch, following superimpositions in the whole 3D arch area. It was possible to display colorimetric maps for qualitative comparison, and the deviations of the values were classified as clinically acceptable. Within the limitation of this study, the clinically acceptable in vivo frequency of points’ deviation, or the precision, was obtained in 98.8% ± 1.4%; therefore, the use of open-source software can be a viable option in the digital workflow, improving patient follow ups with the 3D model superimposition.