Aim: To evaluate and compare six protocols proposed for inferior alveolar canal tracing on DICOM files generated from different three-dimensional X-ray-based radiographic machines using a mutual third-party software. Materials and Methods: Five adult dry mandibles were scanned three times; one was with a CBCT machine (Planmeca ProMax), and the others were with two different MSCT machines (GE Optima and Philips Brilliance). Imaging data were exported in DICOM format and imported to a third-party software. Then, on each scan, the inferior alveolar canal was traced using six protocols by three independent experienced blinded operators with different specialties. The proposed 540 color-coded traced inferior alveolar canals were compared with a gold standard created by experienced operators from radiology and anatomy departments. The comparison was done using a specially designed 6-point scoring system. Results: The cross-sectional and the hybrid protocols showed the highest significant scores with no significant difference between them regarding all the operators and all machines. The sliced panorama-like protocol could give reliable results, except at the mental foramen where it was user-dependent. The fully automatic protocol failed in inferior alveolar canal tracing in all cases by all operators on all different scans. Operators preferred the CBCT machine, although it did not significantly affect the results. Conclusion: The cross-sectional and the hybrid protocols are the recommended protocols to trace the inferior alveolar canal for giving consistent results among different users and different used machines.