Using a hair dryer, dry out the filter until no water remains in it. If you don't get it dry you run the risk of hydrolock or pulling water into the combustion chamber. Either way it's not good on the engine and can damage it.
After drying, replace the filter by putting it back into the airbox lid and fitting the two back onto the top of the airbox. You may find it difficult to get the lid back into place, but be patient with it.
Technique provided by Dude:
"The trick to getting the air filter assembly back in place is this: Look through the space between the frame pipe and the end of the trunk to line up the three prongs - push back, then lower the assembly about an inch, then push back again. You have to lower the filter housing once you've gotten the prongs lined up and partially inserted. You won't be able to seat the filter assembly without LOWERING it and pushing back again."
Once it's down, replace the screws then the engine cover. All done...