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Another idea would be to use a merged cut. If you have the Advanced Assembly extension, you can merge in a model atop another one and cut away instead of adding material, therefore leaving behind the difference. This may be more or less useful than putting two models on top of each other, especially when it comes to internal features. It all depends on the nature/complexity of your model.
Obviously, though, I think comparing two model through the built in analysis functionality is ideal if it works well.
In Reply to Wayne Falco:
Does not sound good. I am waiting to see if i can get the native file.
thanks Doug.