If you have deleted everything from that drive I would assume you want it empty. Just issue a format command on it and that will take care of it
Just to into My Computer, right click on the drive, then FORMAT. That should fix you up. I would not normally, reccomend this but since you dont have anything on it what they heck..
As for your 2nd question are you wanting to boot off of this drive simply by copying and pasting? If you are that wont work. If you are simply backing up the data then we can do it from the recovery console. If you want it to be your bootable OS I would try a disk cloning program such as Norton Ghost or Acronis True Image.