non-manifold mesh generation
 

Hello all

I need to generate a surface mesh for my current CFD analysis. The solver requires internal surfaces for defining region based property. If the surface intersect with actual domain the intersecting sections needs to be removed and outer faces needs to share edges with fluid domain surface mesh to work correctly.

I have attached some pictures to make my problem clearer. Two intersecting surfaces (two stls) need to share edges at the intersecting curve (picture 1 & 2). I am working with mesh mixer and have not found a way to do so. My desired result would look like (shared) but doing the Boolean operation to get this results in removal of the internal part (pic: internal). Please let me know if you have experience working on similar case and if meshmixer is not a viable option than other open source package that i may use.