I usually give mine a couple days before I mess with the babies. My colonies are still pretty newly established. Then I move the mother to another enclosure, clean out any bloody bedding, shift bedding around to distribute my scent so it's not just on the pups, do a head count, put the mother back and leave them alone again. One of my rats just gave birth a week ago to over 16 pups... 16 was where I lost count. That was from just a quick peek into the cage though the screen while I was bestowing a few treats to distract her, rather than opening it and really counting. By the time I did an actual count, it was down to 15 pups. I think there were probably just too many for her to feed, so she thinned them out. She's happily raising the remaining 15 now, and they're all strong and healthy.