Separated endodontics instruments and high-density obturating materials produce metal artifacts on cone-beam computed tomography (CBCT) scans. This study evaluated a novel methodology to detect separated instruments using artifact suppression and color map algorithms with CBCT post-processing software and compared with periapical radiographs (PRs). Endodontic instruments were incorporated into 168 root canals filled with four sealers. Additionally, 40 root canals were only filled, serving as control. CBCT scans were acquired in PreXion-3D-Elite, and digital PRs were taken in distoradial, mesioradial, orthoradial, and proximal directions. The treated teeth were analyzed using an artifact suppression algorithm combined with a color map algorithm. The separated instruments appear in the color map with larger expansion in red to allow identification. This map provides valuable information by showing dynamic visualization toward the point of expansion of the high-density object, hence suggesting a separated instrument. The chi-square test was used to compare the separated instruments among the imaging methods. Bonferroni correction was used for multiple comparisons. Statistical significance was considered P < 0.05. Overall, CBCT performed significantly better than PRs (P < 0.001) in detecting separated instruments. PR was influenced by all the variables studied (P < 0.05). The artifact suppression and color map algorithms, combined with dynamic navigation, effectively identified separated instrument fragments in all the root canal fillings, regardless of filling material, image view, or root canal. Only 32.3% of the root canal fillings viewed by PR detected separated instrument fragments. This method seems to be useful in the resolution of the problem of viewing separated instruments with CBCT post-processing software.