From time to time, depending on your part, residues from the Intersection can appear. This only happens for your Nominal-Geometry STL-File as well as for your retransitioned NURBS-Geometry. The root cause is that per default all Non-Design surfaces grow a little bit beyond their boundaries to ensure a trouble-free and clean intersection. This is done with an automatic detection of Non-Design faces. The left picture below shows exactly such a case.
With the Advanced User Settings the automatic detection of Non-Design faces can be disabled. Thus, no residues from the intersection can appear. Be aware that you have to apply Machining Allowances on all functional surfaces to ensure sharp edges and functional surfaces after the intersection. When no extra material is needed for the post processing of the part a Machining Allowance of 0 mm should be added nonetheless to guarantee the functional surfaces.
Advanced User Settings Command:
automaticFunctionalFacesDetection.positiveNonDesignDirection=false