If the scan have cerec scan bodies then no, has to be done in sirona world, but is scan has, Dess, nt trading, straumann, elos etc yes it can be just need the corresponding library installed in 3shape.
Now the disappearing scan body thing. Trios workflow is scan arch with out scan body and no healing cap, emergence profile scan, then scan with scan body abutmentalignmentscan, then opposing and bite and preop if enabled in order.
Other IO scanner dont adopt this scan flow. Like itero prep arch, opposing and bite. So you must scan the scan body in the prep scan only. But with the newer itero i tell my client add a pre op and scan the prep arch with no scan flag or healing cap to capture the socket for emergence design. then in the 3shape i rename files to get it to work like trios work flow.
But planscan can do the same work flow using pre op scan as emergence scan.
But if you only get one scan with the scan body, and no emergence profile scan, I simply make the same scan into the abutment alignment scan and extract the scan flag out of the scan in the sculpt on prep scan step and create a small socket.
the scan doesn't disappear, it just is used for one purpose, to align the scan flag to the scan. that's all. it is still in the case folder.
so yes it is possible as long as it is not a cerec scan flag.