LoL, you really dont know anything about computers if you belive that.
a full format will blow the entire HD away, not just the file system. that includes the MBR (master boot record)
fyi, no M$ system has root files as there is no such thing as root in M$. root = *nix lowest (or highest depending on how you want to read the tree) level in the tree. nothing can be deeper into the system then root in a *nix system.
so put in your winXP CD, fire it up and do a full install, including format (not quick) NTFS and your virus/worm will be gone. nothing to be left behind.
if you really dont trust, it then pop in a win98SE startup disk with fdisk on it and blow away the partitions on your HD, then recreat them. this makes a fresh MBR in addition to other partion table information on the HD.
after fdisk you can always format c: /s/u
IIRC that is the proper dos command to format the HD as a system drive and unconditional. in other words clean everything off the HD without exceptions. make it all go poof bye bye.
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to do a complete format and erase everything you will need to reinstall your floppy and cd rom drivers to run setup for windows and dos just to be able to use the computer.
how old is this system you are working on? an 8088? since win3.1 days you have NOT, i repeat NOT had to do that to clean any HD, or install any M$ OS. that is unless you are using legacy hardware. now if you are running win95a, you might still have some legacy hardware that is old enough to have to deal with that BS, but if you are running anything newer then 7 years old you will not have that problem.