From awcolley.com

Windows: Fixing the MBR

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Fixing the MBR

This is not really a problem or annoyance with Windows; it is an issue with the boot managers used by Linux (GRUB and LILO being the main ones) when one is trying to remove Linux and go back to Windows-only on a computer.

Twice I have setup a Linux/Windows dual boot system and twice I have needed to remove Linux and return to straight Windows. Both times, after removing Linux, I still got a boot-up prompt asking which operating system to boot.

The first time I just lived with it until I finally got irritated enough to go search the web for how to get rid of GRUB or LILO. The second time, I somehow deleted something that caused my computer, early in the boot-up procedure just before the list of boot options would normally appear, to hang at a screen which displayed "LI" and nothing else --- an indication from LILO that the boot record was fubar.

UPDATE: It has since happened again (at work) when using GRUB. The last screen displayed when the boot process abruptly halts has only the word “GRUB” displayed. This time I wasn’t trying to remove Linux, but that’s another long story.

I learned two things from that second experience:

1. ALWAYS create an emergency boot disk BEFORE you will ever need it. For Win98, I went to the MTSUTILS/FAT32EBD directory on the Win98 CD, and ran the FAT32EBD program. Then, I replaced the MSDOS.SYS on the floppy with the one from C: so that my computer could boot from the floppy into Windows rather than the MS-DOS prompt.
2. To restore the MBR (Master Boot Record), which is what Linux mucks with when it installs GRUB or LILO, use an undocumented feature of FDISK (found in your WINDOWS\COMMAND directory):

      fdisk /mbr

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