make a Windows 98 Bootdisk from Control Panel/Add-Remove Programs/StartUp Disk. Do this on YOUR system on a guaranteed CLEAN system. Then, write-protect the floppy by moving the tab on the back of the diskette to the position where you can see a hole through it. This way, the virus-infected pc (your brother's) can't infect the floppy files, if there's still a trace of it leftover. Anyway, never hurts to be safe.
One file you might want to add to the bootdisk before you write-protect it after Windows creates it is "Smartdrv.exe". It's probably in your c:\windows folder now or c:\windows\command folder. It will speed up the reinstallation of windows from the cd when it's time.
Now, have him boot up with the floppy. It will ask if you want CD-Rom support. Right now, you just want to format it, so use the arrow key and choose
"Without CDROM Support". This way, the diskette will boot up faster. You'll choose CD-ROM support after rebooting following the format.
Now, once the diskette boots up to the "A:\" prompt, type in (without the quotation marks): "Format c: /s" This will format his C: drive, and the "/s" will put the system files in his C:\ folder (Command.com, msdos.sys, io.sys, drvspace.bin).
The format will take a good few minutes...depending on the size of his drive. It will warn you that "All data will be lost", and ask whether you want to proceed...and, of course, you want to proceed.
Now, before you actually format, however, you might want to save a couple of things, like his address book for email. If he uses Outlook Express, it's in the C:\Windows\Application Data\Microsoft\Address Book folder. It's got a *.wab extension...probably his email name followed by .wab (windows address book). Also, if he uses dialup, look for files that end in .dun for dialup networking, or at least have the list of phone numbers for access to the isp.
Anyway, after you save that stuff, format away. Then, it will ask you if you want to format another. Say no, and reboot. This time, choose "CDROM Support". Have the Windows Disk ready.
Just be aware that the diskette creates a "Ram" drive that makes a temporary drive out of Ram for some utilities on the diskette. What this does is move your CDROM letter up one letter. So, if your CDROM is normally drive D:, it's probably going to be E: if you boot with the diskette with CDROM support enabled. It tells you right before the A: prompt appears which drive is the CDROM Drive.
But, for the sake of argument, let's say the CDROM is normally drive D: and you boot with CDROM support enabled on the diskette. When you finally get to the A: prompt, you'd type in:
Smartdrv <enter> (assuming you copied the smartdrv.exe manually to the bootdisk when you created it)
E: <enter>
Setup <enter>
Have the Windows Serial Number handy.
You're all set. Get an antivirus program installed immediately! Also, get something like Zonealarm (zonealarm.com free version) so worms can't even access the net without you knowing it.