1. What version of 3shape?
2. How are you importing the itero files into 3shape?
3. Are you designing the abutment first of just printing the model right off the bat?
I have a specific worklow for itero implant cases.
Most of my docs only scan the arch with scan bodies, opposing and bite. For this work flow i import the file into 3shape. Change order to digital impression, select abutment type needed, add a model to order. Also add a gingival scan to the order. The two teeth icon next to pre op in the upper right are.
Then I press f4 on the case and go to scan upper or lower ad copy the Raw prepartaion scan and paste it making tho of the files. Then i rename the cop to this, AbutmentAlignmentScan Just like that caps and all. Now the case has a gingival scan. Also get rid of the pre op scan in the order.
Next step in design i extract the scan body in the sculpt on prep arch step. And using the wax knife tool create a mini socket, Just need the outline where the tissue is, Now you can align then scanbody and still have the model with the extracted scan body.
Workflow #2, i have the scan the arch with out a healing cap or scan body using the pre op scan, then the prep arch has the scan body. Same order setup as above. Then press f4 go to scans upper or lower as needed, then copy the name of the raw prepartion scan and at the same time rename that file to AbutmentAlignmentScan. Then rename the pre op with the copy of the file you just did. Now workflow is just like trios scan no need to extract anything.
If yo uhave screen caps post it so i have better understanding of what is happening.