The nickel–titanium (NiTi) instruments’ geometry plays an important role in their performance and behavior. The present assessment intends to validate and test the applicability of a 3D surface scanning method using a high-resolution laboratory-based optical scanner to create reliable virtual models of NiTi instruments. Sixteen instruments were scanned using a 12-megapixel optical 3D scanner, and methodological validation was performed by comparing quantitative and qualitative measurements of specific dimensions and identifying some geometric features of the 3D models with images obtained through scanning electron microscopy. Additionally, the reproducibility of the method was assessed by calculating 2D and 3D parameters of three different instruments twice. The quality of the 3D models created by two different optical scanners and a micro-CT device was compared. The 3D surface scanning method using the high-resolution laboratory-based optical scanner allowed for the creation of reliable and precise virtual models of different NiTi instruments with discrepancies varying from 0.0002 to 0.0182 mm. The reproducibility of measurements performed with this method was high, and the acquired virtual models were adequate for use in in silico experiments, as well as for commercial or educational purposes. The quality of the 3D model obtained using the high-resolution optical scanner was superior to that acquired by micro-CT technology. The ability to superimpose virtual models of scanned instruments and apply them in Finite Element Analysis and educational purposes was also demonstrated.