First off, yes, take the male out straight away and he will have to live somewhere separate until at least 8 weeks after he is neutered.
Rabbits are most receptive to a male in the first 72 hours after giving birth, so if the male and the female were living together when she gave birth, then you face another litter in 31 days time. So be prepared for that.
You need to check the nest and the babies to make sure there are no dead kits in there and no placentas or anything.
You can stroke her first and then look in the nest. If she is a stressy bun maybe try and put a dab of vanilla just abov e her nose so she can't smell you, or ask someone else to feed her treats and food she likes while you rummage in the nest.
It's a myth that rabbits reject their babies. So try not to worry about that. She may not know what to do with them, but that's different from rejecting them.
You will need to check they are being fed, but it may take 24-36 hours for her to do that because it will take a while for her milk to come in and she will be inclined to feed them only once or twice a day. She will do this by standing over them for only about 5 mins and you are unlikely to catch her doing it. She will also, by instant stay away from them unless she is feeding them (especially with her first litter).
To check they are being fed you can look at their bellies. If they look like the swallowed a ping pong ball then they are being fed. If they look shrivelled then they are not being. If they are not being, don't try and supplement them because there are a couple of ways to help her.
Make sure she has unlimited hay, and she needs her food increasing from today onwards.
Don't change the nest right now unless it has been used as a toilet previously. If that is the case get something that the mum can stand in and turn around in (for a small bunny a show box can work well), and make sure it is open at the top and has high enough sides for the kits to not get out, and use it as a nest box. Line the bottow with shavings, then move asn much of the current nest as possible into it, and use additionl hay to try and plump it out a bit.
Has mum plucked fur?
How old is she?