How to Format a System Partition in XP
It is not possible to format a system partition by using the Disk Management utility in Windows XP. Because the system partition is the disk volume that Windows resides on, and files cannot be deleted while they are in use, this action is impossible while Windows is running. However, you can format a Windows XP system partition using your Windows CD.
Instructions
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Start your computer with the Windows CD inserted in the drive. If you do not have the Windows CD, skip to Section 2. This Windows installation program will begin to load.
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Hit the "R" key when you see a message saying "To repair a Windows XP installation using Recovery Console, press R."
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Hit the "1" key then hit "Enter" when you are asked which Windows installation you would like to log into. This assumes that there is only one Windows installation present on the computer. Enter the administrator password for the computer, then hit "Enter." You should now be at a screen with the prompt "C:\WINDOWS."
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Type "Format C:" and hit "Enter." You will receive a warning stating that all data on the drive will be lost. Hit "Y" and hit "Enter" again. The system partition will be formatted. This process may take several minutes on some computers.
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Tips & Warnings
Prior to formatting your Windows XP system partition, make absolutely sure that all of your important data is backed up, and that you have another operating system ready to install on the hard drive. Formatting the system partition will leave the computer with no operating system until a new one is installed.