I'd suggest you wait with any pruning until the roses "tell" you what wood is still alive.

Thanks Jean. I don't mean to sound stupid, but how? The stems are all still green. The leaves are infected with black spot or have dropped. My concern now is saving the bushes. They are five year old climbers, if it makes any difference.

Here is a formula to put in the ground and spray the plant itself to help with any fungus happening due to soggy dirt:

32oz. water
2 caps of Neem Oil (dyna-grow brand) it is all natural and organic
use the 8oz jug cap
pour about 1/2 cup of the mix in the soil

Things to help drain the water
1. when all else fails...replant the plants in a drier area
2. try to dig around the outer base of the roses and below the roots and fill the dug out area with course gravel to drain off excess water
3.do this no matter what...push back any mulch on top of the bed to help dry out
4. some potting soils for all use, are bone dry...use that type to place on top of the bed to help soak up the water.
5. check out from the local nursery if alittle gypsum will help dry up the excess water