This is one of the reasons that I partition my drives into the lagest number of partitions I can. What I do is count the letters available, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, = 20, (W, X, Y, &Z, are reserved for DVD Drives and Flash sticks), then divide my available HDD space by 20 to arrive at partition size. I make them all the same size so in the event of problems, things can readily be transferred from one partition to another. Usually it is the "C" partition which gets screwed up in one way or another, whether it be viruses, bad sectors or whatever, because that is where "Windopes" resides.
What you want to do in this case is run an AV program from your CD ROM drive, because the only other way I can see for you to clean up this mess is to "Format C" which is where the virus WILL be found. EDIT : (Correction, thought of another way to cleanup your mess if you have another HDD you can use temporarily. See end of post)
In my case, I go to some lengths to move other software to "D" drive which is named "Software" in my machines, and contains :
1) Downloaded install programs of all kinds sorted by types,
2) Motherboard files : Bios updates, Manual, and Utilities for various types of Mobos
3) Licences : A folder containing the various serial numbers for the software I hold licences to use
4) Windopes Update installation files
5) Hardware Driver installation files and related software supplyed by the hardware manufacturer.
6) An XP Software Folder which is subdivided into the following folders :
a) Artwork : Which contains all programs related to Pictures
b) Audio : Which contains all programs related to Sound.
c) CD Creator : Which contains all programs related to burning CDs and DVDs,
d) Games : Which contains all Game installs. (Though I am not big on games.)
e) Internet : Which contains all programs related to browsing the internet.
f) Utilities : Which contains all utilities, INCLUDING Antivirus.
g) Video : Which contains all programs related to Video playback and editing.
h) Writing : Which contains all prgrams related to writing.
Needless to say, my "D" partition has its own backup partition which on this machine is "Q". Further I make it a practise to locate "D" as the front partition on a drive other than the one holding "C", This speeds up operation, and since I do the same thing with my swap file, it means that when you are running a program under "Windopes" instead of having one set of read heads wearing themselves out chasing back and forth over "C" drive between "Windopes", The "Windopes" swap file, and the program you are running, you are using 3 sets of read heads, one for each of the 3 items being accessed; = FASTER.
Another thing about this setup is I can format "C" if I have to, with minimal loss; since all that resides there is "Windopes" and its most closely related functions.
Getting back to your problem, you could try taking the drive out of the machine, substituting another drive, running a "Windopes" install on that drive, (complete with antivirus install), then reinstall your infected drive set as a "Slave", and run the antivirus program to check it.