There are some varities of "viri" that are very difficult to remove and one method that has always worked for me is to employ what I call the "zombie clone" method.
On a drive you KNOW is infected with a windows "pathogen", clone any known clean drive over the "infected" drive using clonezilla and make sure to say "yes" to copying the BOOTLDR.
This wipes "everything" that was previously on the drive.
The Virus will not affect clonezilla which is Linux (debian) based
AND runs from a CD-ROM disc
Another method has been to install that Hard drive into any computer with no other hard drive installed and feed the computer virtually any windows installation disc and run the installer, using "advanced options" Delete all previously exsisting partitions and let the installer format the drive... what Windows OS you use is entirely irrelevant because this method of "cleaning" the drive is called "the Waster Installation" method.
as it overwrites everything including the BOOTLDR by default
it's crude but effective (like most crude solutions are)
MY Father liked to run "Scan disc" and other utilities to check the physical condition of hard drives but I found a more reliable method...
IF you copy the drive FULL of data files, mp3 files with included CRC error checking, then copy the files from the questioned drive to another drive
the copying software I use (an old DOS based program called Ztree)
will interrupt the copying operation of the CRC's don't match on even one file.
IF the drive is then formatted and the process repeated and the CRC error happens on the same file again you have a pretty hard indication that there is a physical error on that specific position of the hard drive.
Again the method of testing may be crude but it takes minutes instead of hours to generate a presumptive indication of a fatal problem
and most importantly if you make a third and forth attempt with a different collection of files and you get an error in the same approx location of the drive you have demonstrated "repeatability" that cannot be argued against.
...shortly followed by a whistling sound as the drive in question follows a ballistic flight path towards my (large) recycling bin.
I've also been known to use the "Wasted installation" method to test drives, if the installation crashes
more than once before a Windows XP installer from a known good disc in a known good optical drive
the hard drive in question either gets RMA'd (if in warranty) or sh!tcanned (if NOT in warranty)
in my experinence physical hard drive failures or "errors" account for more than 90%
of all computer issues.
For some reason people find it more comforting to believe in some random act of malice
to simple (random) physical failure.