HELP: Support material prevents model from working correctly

[diaruga11]

I keep trying to make this print correctly, however the support material from the printer places supports inside holes where I am unable to take the support material out and prevents the pieces from fitting together.

3d Printer is a Makerbot Replicator 2 that uses PLA.

Any suggestions to prevent support material from being printed in these places?

[stevendm]

If you are using Simplify3d you can manually place the supports (as opposed to having them automatically generated), thus avoiding the problem areas.