Seperating them once the babies are born is too late, it's best if you're going to seperate them to do it a week before she pops.
It's not ususally necessary to separate them unless you cycle breed, it may help, but usually isn't necessary.
I have a few more questions, like what bedding you're using?
(Pine and cedar aren't good for rats.)
Are your rats sneezing? Itching?
What fat% and protein% is their food?
What is the temp of the room they're in?
Did you give the rats nesting material so the babies aren't on the cold floor?

Rats are usually pretty good at raising their young, but first time mommies sometimes let the first litter die from lack of experience.
Also, unless you need full grown rats, I try to make sure that the nests stay about even, don't let one mommy steal all the babies and then they all die because the others can't feed them.
Certain strain of rat aren't good for breeding, like hairless rats.
Anybody else got ideas?

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