The newer Ford oval emblems aren't covered with a separate clear shell, and I've had trouble finding information about them as well.
You can sometimes find kits on ebay to do this, but they're usually for the older emblems: http://search.ebay.com/ford-emblem-decal
Other than that, you could try working with UV-resistant plexiglas.
You can sometimes find kits on ebay to do this, but they're usually for the older emblems: http://search.ebay.com/ford-emblem-decal
Other than that, you could try working with UV-resistant plexiglas.