How To Delete Second Installation

I have 2 hard drives, and my main hard drive has now become my secondary. I have managed to delete almost everything on the drive, except three mischievous undeleteable files. There is $RECYCLE.BIN, a folder called Boot with BCD and BCD.LOG which are to my efforts undeletable, and a folder calls System Volume Information, which seems to replicate itself each time I delete it. How can I delete these files? I have tried formatting, however windows will not let me format. Taking ownership does nothing to them. When I try to delete BCD or BCD.LOG: "The action can't be completed because the file is open in System."