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Help with freezing transformations

I got same problem described here:

http://www.digitaltutors.com/forum/showthread.php?31792-Is-there-any-way-to-scale-a-skinned-model-and-freeze-transformations




My rig and controllers have transformations on them, mainly the global control, that without them, would have my joints positioned incorrectly. This happened because I borrowed a rig from a different character. The global controller has scale, rotate and translate transformations, that situate the hierarchy to new character. Im using maya.

i can not detach skin and freeze transform as global controller "tells" the rest of hierarchy where to be. How to fix this so i have a clean hierarchy that can be read by other programs? I can detach skin, but would like to not redo the joints.

Bascially would like to know how to freeze transform joints after theyve been set up.

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