Clean up what you can and if necessary, use a 10% bleach and water mix to clean the floor up. But you will have to rinse it well and let it dry before you put them back in.
Are the babies in a nest box? I think that you should pick up the kits and put them in a box, (shoe box is fine). It just has to be big enough to let her in and room to turn around, sides low enough for her to hop in and out, but not low enough to let the babies crawl out. The nest box should be placed in the same spot that she kindled the babies. The box will keep the babies together and warm (especially since they may only be 2) and that way, no one crawls off and misses a meal.
Edited for spelling... duh!