I just use a little hand saw while I hold the base with pliers for a good grip, you can use bone cutters but make sure they are beast or you will just pinch the coral and fubar it all up. Also I have seen people use dremels but I never have so can't recommend that. Make sure you cut it at the very bottom of the stalk closest to the rock it's on.
I would remove all of them but that's just me. It will give you more flexibility in the end where to put them in your tank. Some corals like to be in particular spots and others do not like it. I always try to avoid buying coral bundles for that reason.