Quick answer ... you can't. Never run a low-level disk utility from within a multi-tasking operating system such as Windows or Linux. Other programs running in the background could interfere with the utility. Reboot the computer from a floppy first.
You should never attempt to do a low-level format on an IDE/ATA or SCSI hard disk. Do not try to use BIOS-based low-level formatting tools on these newer drives. It's unlikely that you will damage anything if you try to do this (since the drive controller is programmed to ignore any such LLF attempts), but at best you will be wasting your time. A modern disk can usually be restored to "like-new" condition by using a zero-fill utility
Hard drive manufacturers have created for modern drives replacements for the old LLF utilities. They cause some confusion, because they are often still called "low-level format" utilities. The name is incorrect because, no utility that a user can run on a PC can LLF a modern drive. A more proper name for this sort of program is a zero-fill and diagnostic utility. This software does work on the drive at a low level, usually including the following functions (and perhaps others):
- Drive Recognition Test: Lets you test to see if the software can "see" the drive. This is the first step in ensuring that the drive is properly installed and connected.
- Display Drive Details: Tells you detailed information about the drive, such as its exact model number, firmware revision level, date of manufacture, etc.
- Test For Errors: Analyzes the entire surface of the hard disk, looking for problem areas (bad sectors) and instructing the integrated drive controller to remap them.
- Zero-Fill: Wipes off all data on the drive by filling every sector with zeroes. Normally a test for errors (as above) is done at the same time.
Only use a low-level zero-fill or diagnostic utility designed for your particular hard disk. You can download one for free from your drive manufacturer's web site. Even though damage probably won't result from using the wrong program, you may lose data and you may also complicate any warranty service you try to have performed on the drive. (Technical support people at "Company X" generally don't like to hear that you used a utility on their drive written by "Company Y".)
I hope that this helps you out a bit.