Name X

in PW 2014:

In IMInspect:

- Scan first half of part in a mesh.
- Physically move the part
- Create a new device position with (custom)
- Scan the second half of the part

- Best Fit Data to Data with the two scans from different device positions.  Hopefully you've scanned enough common spots for these scans to merge
- Under Tools > Data Objects > Create Polygonal Models:

we want to use this data tool, as it samples the source meshes' underlying pointclouds to create the "composite" mesh, rather than just combining the two source meshes.  This method is more desirable for accuracy.

source:  PolyWorks Technical Support, when I had this exact issue

easiest way for me would be:

collect the data in IMInspect
create the coordinate system as desired
export data to IMEdit for repair / optimization / smoothing / meshing / reverse engineering

I think the coordinate system COULD be altered in IMEdit, but it's not as intuitive.  Check out Tools > Alignment > Manual Alignment.