Backup
In case anything goes wrong, it's always good to be able to start over. To this end, make a disk image backup using a bootable CD, or any other bootable media such as a flash drive. Since the computer has been compromised, it's best if the image backup is made to an external device, typically CDs, DVDs, a LAN resident computer or an external hard disk. If you have partitioning software instead of disk image software, then shrink the Windows partition and copy it to a hidden partition on the hard disk.