How a setup is built from a segmented scan
A raw intraoral scan is a single continuous mesh. Before any tooth can be moved it has to become individual objects, so each crown is separated along the gingival margin and the interproximal contacts, and the missing surface below the margin is reconstructed to a plausible anatomical form. Where the scan is short of data, typically the distal of second molars or a contact closed by heavy crowding, that is flagged rather than guessed at.
Segmentation quality decides everything downstream. A crown separated too far apically overstates the interproximal enamel available and makes IPR figures optimistic. A crown separated too coronally hides the contact point that actually limits movement. A long axis is assigned to each tooth so that tipping, torque and rotation are measured against something consistent rather than against the mesh.
With the arches articulated from the bite scan, the pre-treatment record is complete: crowding measured per arch, arch form recorded, midlines related to each other and to the facial midline from your photographs, and the existing overjet and overbite noted. The setup is built on that record, and the movement table you receive is the difference between it and the planned finish.