I received a reply to this from Michael. I am posting it here for others:

Hi Simon – mesh topology is inherited from the UV grid structure of the “underlying surfaces”, which are the base surfaces used in a NURBS model. The way NURBS modeling works at a fundamental level is that a surface is made up of a regular row/column grid of control points which defines a UV layout to it, and then there can be trim curves that mark various zones of that surface as either an outer trim boundary or as an interior hole.

When MoI goes to make a mesh from a surface, the meshing process first generates quads along the UV directions of a surface, and then those become n-gons where the quads hit trim boundaries.

When you split an object by doing a boolean or a trim operation, it’s a fundamental feature of NURBS modeling that those “underlying surfaces” remain exactly the same as before and it’s only new trim curves that are created on the surface. That’s why Booleans work so much better in NURBS modelers than in polygon modelers, because boolean operations don’t cause things to fragment into a zillion little pieces for every individual cut.

But because of how that structure works it is normal that you will not see changes in topology just by splitting an object.

Really the best way to influence topology is to process the output mesh with retopology tools in a polygon modeling program. That’s the standard way to achieve any particular desired polygon topology and you should not generally expect to generate a hand tuned topology from an automatic generated mesh.

It is possible though to influence the topology in MoI by reconstructing specific surfaces by extracting edge curves by selecting the edge and running copy/paste on it, and then delete your trimmed surface and construct a new surface using something like sweep or loft which will generate an untrimmed surface as its output which will then mesh with a topology that follows that particular new construction.

Like in your example there delete the strip piece, and then select the 2 edges that are now open, do a loft between those to build a new simple untrimmed surface and then use Edit > Join to glue that new surface into the original structure. Now the exported mesh will be different in that area, the edges of the surface will be natural edges of the underlying surface rather than trim curves on some larger extended underlying surface.

But really it’s best if you need specific topology to plan to do retopology in your polygon modeling toolset.

Hope this helps give you some tips though,

Now that I read your question again it looks like I didn’t quite answer you directly, you asked:

“In the picture below I have had to split the object into separate parts to achieve this but that means I would have faces in unwanted places when I export.”

There is not any way to have mesh generation influenced just by some curves on a surface, and it’s not really influenced heavily by splitting either since as explained above that just introduces new trim curves but keeps the same underlying surfaces. If you want to influence the mesh generation you would need to not only split objects up but also reconstruct key faces as untrimmed surfaces by building new ones using loft or sweep tools and using the curves from the split as part of the inputs for the loft or sweep.

If you need to influence the mesh topology to have particular edge loops, you should expect to that during a retopology stage in your polygon modeling program. That’s not something that is going to be controllable with the mesh export out from MoI.

The mesh export out from MoI should be suitable for rendering directly without needing to have any specific topology to it though, you generally only need specific types of topology if you want to apply sub-d smoothing to an object but usually with NURBS models they are already in their final form with smoothing already applied as fillets and so it typically does not really make sense to try and further smooth a NURBS CAD model…

- Michael