The inaccurate maxillomandibular relationship of virtual casts following alignment by the vestibular scan may result in intersection (intermesh penetration) between opposing dental arch surfaces. Intersection occurs at short interocclusal distances in the occlusal contact area (OCA) and may result in infra-occluded definitive restorations. The purpose of this clinical study was to compare initial (by the proprietary scanner software) and new alignments (by a standalone 3D software) of virtual casts regarding OCA and intersection failure. New alignments aimed to rectify intersections by refinement of occlusal contacts. The virtual casts of 30 patients following digital and conventional impression-taking were analyzed, which were acquired for single implant restoration in the posterior site. Digital impressions were performed by both IOS 1 (3M True Definition) and IOS 2 (TRIOS 3), either as complete- or partial-arch scans, respectively. Mounted gypsum casts were digitized as complete-arch by a laboratory scanner (LS) in enabled and disabled mode to avoid intersection [LS (+)/LS (-)]. All virtual casts were newly aligned by a 3D software. The difference of the OCA and the area of intersection were calculated for initial and new alignments, using interocclusal distance ranges of 0-100 μm, 0-10 μm or <0 μm (=intersection). The difference of the OCA was compared using a linear mixed model. The distribution of occlusal contact points per modality and alignment was assessed independently by three observers and estimated by inter- and intraclass correlation (ICC) coefficients. Virtual casts following initial alignment demonstrated intersections irrespective of the modality. The mean area of the intersection was most for IOS 2 (79.23 mm2), followed by IOS 1 (48.28 mm2), LS (-) (2.77 mm2), and LS (+) (2.01 mm2) in partial-arch scans. Complete-arch scans demonstrated an area of intersection of 70.63 mm2 for IOS 1 followed by 65.52 mm2 (IOS 2), 6.13 mm2 [LS (-)] and 2.76 mm2 [LS (+)]. Newly aligned scans showed no intersections. The overall distribution of occlusal contact points demonstrated moderate reliability (ICC 0.63). Good reliability could be observed (ICC 0.9) for LS (-) scans. Intersections in the area of occlusal contact points are a phenomenon restricted to virtual casts, which should be considered in CAD/CAM. Initial alignments of LS are less affected by this virtual phenomenon, and contact points may be more distinct according to their anatomic region compared to IOS. Furthermore, intersections can be rectified in a 3D software by adjustment of the maxillomandibular relationship.