No it only clears the BIOS settings. It does not change anything on your hard drives.
Note though you may have to go in and set your HD as a boot device again, but that's it. Once you have the BIOS settings set back up it will work fine. Also note that you need to have the settings the same as when you installed Windows, otherwise you will have problems (Particularly the HD setup, if they were setup as SATA / RAID / AHCI they need to be put back, or windows will BSOD).