One way is to use MAT Pose Edit from freestuff here to create your MAT pose files. In the list of materials you can select the materials you don't want to affect and delete them so they don't appear in the MAT pose. If you're doing it manually with a text editor, I'm sure you can achieve the same result by simply deleting the relevant material lines. I always use MPE so someone else will have to tell you exactly what to delete. :-)

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