I'm using the program called ClamXav.

First off I must ask, why are you running a virus scan on an iMac?
Yes, there are viruses for macs, but they aren't very common. You have to have downloaded, ran, and installed the virus for it to affect your Mac.
Macs can, however, be considered "carriers". Which means, Yes your mac does have a virus but it isn't affecting you in any way. It's just there. In this case if you happen to send an e-mail, the virus will be sent to the recipient. If the recipient happens to be a PC user, the virus would affect them.

To answer your question, if it says that it's scanning the Hard drive, it is scanning everything that is on the hard drive, including all of the files and Mac OS.
It wouldn't be scanning the bios or hardware.
In my opinion, if you're not having any trouble out of your computer, a hard drive scan is perfectly fine to dispose something that may affect an e-mail recipient.