A very common issue for a new user of Intra-Oral Scanners is to appreciate that, generally, the cameras nor the software, can tell the difference between tooth structure and soft tissue.
Furthermore, once soft or hard tissue is captured by a scanner, it assumes that the data is part of the model and part of the “equation”. What this means for automation is that this data, if you don’t take it into consideration, can actually hinder the automatic stitching of arches to each other via the buccal bite.
In the attached video, you can see how some excess data in the lower arch, namely the cheek, prevented the automatic stitching of the buccal bite with the upper and lower arches. Simply trimming away data sets that are in the line of sight for your camera can greatly speed up the process.