There's no specialized prison to deal with alchemists that I know of. So long as you take way their ability to draw or use transmutation circles, most alchemists aren't any different from locking up anyone else.
I guess it gets more complicated when you have people like Kimbley. He's an alchemist who has a part of a transmutation circle tattooed on the palm of his hands. When he brings his hands together, it completes the circle so he can transmute. There are hand cuffs that are used to keep people's hands apart though, so he'd be pretty defenseless if those were put on him.
[They're also effective to keep Ed from transmuting, but he's not about to spill all his secrets.]
no subject
I guess it gets more complicated when you have people like Kimbley. He's an alchemist who has a part of a transmutation circle tattooed on the palm of his hands. When he brings his hands together, it completes the circle so he can transmute. There are hand cuffs that are used to keep people's hands apart though, so he'd be pretty defenseless if those were put on him.
[They're also effective to keep Ed from transmuting, but he's not about to spill all his secrets.]