The intended design can be found here: http://www.thingiverse.com/thing:630314.

You are correct, there is a large amount of support material that needs to be removed. However that is not the issue. I realized that I can solve the support structure issues by changing the orientation of the item to lay flat, this is preclude the use of supports. However the areas I am concerned about are the areas with no support but appear somewhat stringy and rough.