1.Your HDD details? Manufacturer/ Model / capacity
You can then check the manufacturer's website for the relevant HDD Diagnostic/repair tool most of which can wipe your HDD clean and restore it to factory condition. For example Seagate's SeaTools for DOS, Western Digital"s Lifeguard Data Lifeguard Diagnostic for DOS.
2. If you have more than one partition on the drive and have data on it and would like to reinstall the OS only on the System Partition, then you can run Partition Wizard Home Edition 8 from the bootable CD/pendrive, try MBR rewrite and then format only the System partition and check whether your problem is resolved.
Note: Even Partition Wizard can wipe your drive.
With no specific details on the above two aspects, I can only give the above general guide lines..