Mike,
I am sure that J. Baker will correct me if I am wrong but I was told by my instructor that the MODEL reference set was a special reference set that would be automatically created even if you deleted it. Under customer defaults you can set what gets put into this reference set automatically. He recommended that we create our own reference set in which we could control exactly what was and what was not in it. In our seed part we created a reference set named "DESIGN".
If you want to remove all items from the reference set, then select the "Deselect All" button from the selection tool bar . Now you can select the items that you want in the reference set.
Regards
Jurgen
NX 9.01 Win7 64bit TC10.1