We aimed to evaluate root parallelism and the dehiscence or fenestrations of virtual teeth setup using roots isolated from cone beam computed tomography (CBCT) images. Sixteen patients undergoing non-extraction orthodontic treatment with molar distalization were selected. Composite teeth were created by merging CBCT-isolated roots with intraoral scan-derived crowns. Three setups were performed sequentially: crown setup considering only the crowns, root setup-1 considering root alignment, and root setup-2 considering the roots and surrounding alveolar bone. We evaluated the parallelism and exposure of the roots and compared the American Board of Orthodontics Objective Grading System (ABO-OGS) scores using three-dimensionally printed models among the setups. The mean angulation differences between adjacent teeth in root setups-1 and -2 were significantly smaller than in the crown setup, except for some posterior teeth (p < 0.05). The amount of root exposure was significantly smaller in root setup-2 compared to crown setup and root setup-1 except when the mean exposure was less than 0.6 mm (p < 0.05). There was no significant difference in ABO-OGS scores among the setups. Thus, virtual setup considering the roots and alveolar bone can improve root parallelism and reduce the risk of root exposure without compromising occlusion quality.