Its quite simple buddy. boot ur system in windows as you normally do or in case you are not able to boot in windows then boot through a bootable windows cd/floppy.
Now go to your primary partition (which is usually C
and then type
(case does not matter). This will cause the MBR to be overwritten by the WINDOWS OS.
Now when you boot the PC , no boot loader will be there insted it will be booted to windows directly.
Now you safely use your bootable floppy.
BUT be sure you have the bootable floppy ready with you .