Is there way to achieve this with the 3D Slicer ?
First makes scans of upper jaw and lower jaw and then export them as stls (because thats the only available option)
Then is there a way to get them registered in to occlusion by adding corresponding landmarks in them.
You should be able to do that using the Fiducial Registration Wizard in the SlicerIGT extension.
This powerpoint from Perklab lays it out nicely
I will try it but i am not exactly sure how it will work on this.