Change the drag model
Change the drag model because drag is not all about the parts in front of the plane but a lot about how the plane ends.
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Thomas commented
http://www.simpleplanes.com/a/Y5pd5o/SR-71-Black-Bird-Short
http://www.simpleplanes.com/a/rOTGXu/SR-71-Black-BirdTo me, I may be wrong but if you smooth the rear of the plane you should reduce the global drag.
You increase the friction drag (because the wet surface increase) but you decrease the pressure drag as you "fill" the low pressure area. But the effect on the pressure drag is greaterIn my case, I just cut the rear of the plane and the global drage is reduced.
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Can you provide some more information? If you can upload an airplane and link to it here I can take a look at it.