The dealership should have reset the codes, but you can go to AutoZone, Pep Boys, or any other auto parts store that will read the codes, and they can reset them for you. An OBD-II scanner should also be able to reset them.
If the codes come back, you'll probably need to have the O2 sensors or cats replaced; if the misfire was bad enough long enough, it's possible that the cats got cooked (a misfire can allow raw gasoline to enter the exhaust stream, which will kill catalytic converters in short order).
There's a long Federally-mandated warranty on the cats is 8-years/80,000 miles, so you may be able to get them replaced (if they're bad) for free by Lincoln.