Did you use the slice tool to make more vertex points? If yes, that may be the answer to your question. When you are in editable mesh and use the slice tool, it will actually create like dubble the amount of vertexes then you really want. Maybe theres a way to fix it, but I know a way to work around it. Use editable poly instead. Then you have much more options to edit the polys, vertexes and the slice tool works properly.
Another sollution to your questin mught be the smoothing groups. If u used the extrude function, the smoothing groups would not be set for the extruded polygons. How to fix it? In your modifier panel, go to the bottom and you'll see a bunch of numbers. If u click on one of the smooth polys u'll see one of the numbers light up. Simply select all of the unsmooth polys and give them the same smoothing number.