How can I delete a system?

A couple of years ago I had trouble with my HD so to play safe I installed another one and put a new system onto it. I meant to use it for a few days to make sure it worked and then delete the old system, but I forgot! I know most people say you should never have two systems but it's never given me any problems.
The troublesome drive seems Okay now so I've decided to empty it and use it as a scratch disc but I can't delete the old system folder. It says it's a read only file and belongs to the system so I'm not allowed to touch it.
Anyone know how to get rid of it?
Thanks in advance.

Okay you caught me! When I said "empty the drive and use it as a scratch disc" I meant NEARLY empty the drive. There are a couple of old programs that I use occasionally and I can't find their install discs.
Is there any other way of deleting a system folder?

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