It's been a week and a half now since i got my rescue rabbit boo. I have gradually increased the size of his play area so that he can get acustomed to his new environment. To start of with he did not mind being stroked and only struggled slightly when being lifted back into his basket. Now that he has full run of the living area (only being put in his basket when im not there to supervise him or when im cooking) when i go to pick him up to put him back in his basket he bolts and stamps his feet. Is this because he sees me as a danger or because he is disapproving at being ut back in his basket? He doesn't show any signs of aggression and binkies alot it only seems to be when he knows he is going back in his basket have i just gave him too much freedom too soon?

He's probably saying, "hey! I don't want to go back in!" Foot stamping can be a bunny's way of signalling danger; so it could be that maybe you startled him trying to pick him up, or it could just be his way of protest. I read that it's good to let bunnies hop in to and out of their cages on their own free will as much as possible, that way they feel like the cage area is their home. If we put them into their cages they might interpret it as a punishment. What I try to do, is tempt my bunny back in with some veggies or a raisin treat, and they he goes in when I want him to, but he thinks that he's making the decision. This took a while at first, but now it's pretty easy--he often just zooms in (he loves veggies!). This way, the cage just becomes another happy place for him, and not taking away his freedom.

If it's the kind of cage that he can't hop in to on his own, maybe you could call him over with a treat and pet him for a second before picking him up, just so he can get used to the idea. We're big on bribing here in my house.

Good luck with your beautiful boo!

Tallullu  - Tabby is right on!  Bunnies thump when they feel threatened and when they protest something.  For example, I dropped some greens into Jack's pen, and then I realized I hadn't rinsed them, so I took them out.  Well he started thumping.  He didn't approve of that at all!  

So, your bunny thumping is just his way of communicating and it has nothing to do with giving "too much freedom"  He may thump just to let you know he's not happy with what is about to happen and that is just part of his personality. So Tabby's idea of enticing with a treat is a great one.

Mine now know the word "treat" and come running into their pen when I say "Treat Treat!"

So when you are giving him a treat - just say the word and soon he'll associate it with that word.