Just take out the adults like normal then take the babies out and put them somewhere secure. Clean your tank then return the babies and adults.
If your rats are eating babies, are they being fed a good diet? Sometimes they eat babies when they don't get enough protein. But if its too much of a hassle to deal with, then I would feed them off.
It's not a hassle, I was just curious. We just started out, yes they have good diet. It was first litter of one, and after cleaning cage, found him killed next day. Not sure who did it.