Good day, I have similar situation in all Cases with cutting model (using boarders in Model's property - draw or select polygon) or importing another contours (sdf, shp ...) - and I must delete points in object that goes farher that surface.
I think - it's global problem of IW (because IW can't add to object's geometry new point (as f.e. work "broader" = structural line in Civil 3D's Surfaces))
Other visible problem - when boarder going through building - and it was no cut.
May be there is command to Java - delete parts of problems objects automatically...
Best regards,
Egor Grebenyuk,
JSC "Roszheldorproject", BIM specialist (infrastructure)
