Hi Rudl, it's quite difficult to place planar quadrilaterals along curved outlines because it's so easy for the 4 points to be warped a little bit. It's most natural for only 3 points to define a plane instead of 4 points.
Have you looked at Rhino's paneling tools? That's a set of tools in Rhino for helping to generate planar quadrilaterals on walls and things like that like you're trying to do here. I think they've had a developer specially focused on working on it for the past few years now. http://wiki.mcneel.com/labs/panelingtools
For doing it manually without any kind of helper tool like that, I guess you'll probably need to do something like initially start with 3 sided areas since you know those will be planar and then figure out what you want to adjust in order to bring 2 adjacent triangular planes into a single planar quad. I believe that the paneling tools has various mechanisms where they go through that kind of a process and automatically adjust points for you or something like that.
Since MoI uses the same file format as Rhino it should be easy to use your surface with Rhino's paneling tools, you can just open up the same 3DM file in Rhino and use those tools on it directly I think.
- Michael
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