TRAPPING SQUIRRELS THAT HAVE BABIES Can you continue trapping babies?  Of course you can!  As long as they enter your trap, just resume your trapping campaign, dispatch each and every squirrel you catch. When you get mama bear, then go back to the nest (if you can) and physically get each of the remaining babies.  No males will be around to "defend the nest," mother squirrels do not associate with other squirrels during this time of their life. Unfortunately, sometimes the nests are difficult to reach, constructed purposely that way.  Females will abandon the nest on your close approach, so if you can reach the nest, sometimes you can chase off the mother and take care of the babies, letting your trap collect the mother on her return.   WHAT TO DO WITH THE BABIES If the "babies" are actually babies, even fully furred, with their eyes already open, they will probably be quite unafraid of you.  Normally, when the mother squirrel leaves the nest for any reason, the pups remain together, all curled up, awaiting the return of the mother.  It would be best, when you did this, for there to be one visit to the nest. Sequential visits (and exits) may cause the babies alarm and they may crawl off in different directions before you can get them all. The best way to handle it (are you ready for this?) would be to asphyxiate each one, as soon as you pick it up. I use a standard pair of leather work gloves, pick up each animal around the midsection and SQUEEZE!  (The heart stops instantly.)  Keep squeezing for at least a minute, until you're sure that the animal has expired.  I then put the animal in a small bag and retrieve the next animal until I have taken care of all of them. If the mother is still around, I leave a trap for when she returns.