Aim: To assess, using the principle of three-dimensional (3D) coordinate metrology, the location and degree of surface damage or wear of two commercially available engine-driven nickel-titanium (NiTi) files after clinical use. Methodology: A total of 24 engine-driven NiTi endodontic files, 12 rotary (ProTaper, Dentsply Maillefer, Ballaigues, Switzerland) and 12 reciprocating (Reciproc, VDW, Munich, Germany), were collected after clinical use. A coordinate measurement dental scanner was used to capture the 3D coordinate data of each endodontic file surface. The surface data were subjected to 3D analysis using a 3D free-form surface analysis software package, which involved the surface interpolation, registration and subtraction of each image of the scanned surface to a baseline 3D image of a new, unused file. Three representative points at the coronal, middle and apical third of each sample were selected to assess any differences in surface damage or wear between the two file types. The reproducibility of the methodology, the measurement of new, unused and used engine-driven NiTi files, was tested. Results: The reproducibility of the methodology was excellent, with a depth difference of 0.002 mm for the new, unused files and 0.005 mm for used files of both types. Reciprocating files generally showed greater surface damage in comparison with rotary files. Furthermore, reciprocating files showed greater wear in the apical third and less wear in the coronal third. In contrast, rotary files had greater surface damage in the coronal third, decreasing towards the apical third. Conclusions: 3D coordinate metrology provided an objective, reproducible, more economical and non-destructive method for assessing the surface damage or wear of engine-driven NiTi files after clinical use. There was more damage seen with files operated in reciprocation compared with those operated in continuous rotary motion. The file operating motion and surface contact at different stages of root canal preparation may account for the differences in the degree and location of surface damage. Keywords: NiTi files, ProTaper, Reciproc, surface damage, 3D dental scanner