Is there a safe way to completely reformat a removable drive

As some of you already know I am reformatting all my drives due to the Virut infection. I reformatted my flash drive via the right click context menu option on the drive letter. Since I have Virut and it spread to all my drives I wanted to make sure nothing at all was left on the reformatted drive(and this would be the same case for my external drive) because of the nature of this infection (perhaps since the hidden stuff that is made after a reformat in this fashion is just a System Restore folder containing a .log and system file and this malware has not been known to infect such file types, I may be just being paranoid) I would prefer nothing at all was left on the drives after formatting them. I was wondering if there was a safe way to do this or am I just being paranoid? I considered trying programs designed for reformatting drives but since the malware infects .exe files I am cautious about that option. I have disabled autorun on all drives via the registry(and naturally I made a backup of the registry and a System Restore point beforehand) and it seemed to work and without side effects, because it happens to safeguards the reformatted drives from being reinfected drive my main drive(or should I say partitions) most likely again perhaps I am being paranoid about this. System Restore was already turned off on both my external and flash drive so I'm confused as to why a System Restore folder at all was made on the flash drive after reformatting it. I tried again after turning System Restore off completely(I'm going to doing a full reformat and reinstall today, otherwise I wouldn't normally risk such a thing) but it still happens. I plan to reformat and reinstall Windows as soon as I have reformatted my flash and external drive after first seeing if I'm being paranoid about this or if there is a way to do what I'm asking safely.

P.S The description of the system file in the System Restore folder is MountPointManagerRemoteDatabase

I can understand the caution of not wanting this to come back, but assuming you were given a clean bill of health from the pro's, logically you are only being forced to do this now due to corruption, with a clean bill of health there should be nothing there to come back again.
A quick search of that file seems to suggest it is a system restore file check point, and as such will appear EVERY time, what I am not sure about is if you turned system restore off if that would stop that until your happy all is well, of course doing this means ALL restore points will be gone, but it's up to you if you want to try this.

Personally if it were me, I would add each drive as a slave to another system 1 at a time and format them in that, I appreciate your concern about spreading any left over infection to other systems, but if you have been given a clean bill of health you should be fine.
When doing this I would approach it the following way, I would get the HDD Low Level Format Tool and install it on a clean system, it is a windows based format tool, BUT, it is extremely powerful and MUST be used with EXTREME CAUTION, because with this tool you can format the OS drive even while using the drive, and the most dangerous bit is you are not asked if your sure you want to format that drive, the second you click format (instruct it to start) thats it, so make sure you triple check your drive letters when using this and ensure you select the correct drive when formatting.

Now thats the tool explained, it's the most powerful format tool available to us ordinary folk that I'm aware of, so it will really wipe the drive to remove remnants of ANYTHING left, adding the drives as a slave should be safe, but NEVER attempt to physically enter the drive, not until the format is complete anyway, that way any remnants of infection "IF" they remain should not be able to cause damage, it's the method I use with seriously infected systems anyway.
You repeat this with all the drives concerned, it will take a long time as it's a very intensive process, but it wipes everything, now while this is happening, remove the mains lead off the infected system, remove the CMOS battery, and move the jumper to the clear position, now l;eave it like that until ALL drives are formatted and reinstalled, the reason for this is if there is a memory resident infection this will take care of that, it's belt and braces as we say, but it's the only sure way to make sure the infection is totally gone, hope this helps.

*edit
Forgot to say once the drives are formatted and your ready to start the infected system up again make sure you return the jumper to the correct position etc, it may seem overkill leaving it on clear for so long, but with such an infection it certainly can't hurt, don't forget to reset the bios correctly with time\date etc on first boot as well.

Thanks for the advice but I have already reformatted my flash and external hard drives and reformatted my main system and things seem to be going fine. I used the Recovery Console to do the formatting without once booting back into Windows, then proceeded to reinstalling Windows. I currently have autorun on all drives disabled as well as autoplay(or are they the same thing?) to avoid spreading such an infection around to other drives if for some reason(and I really hope this never happens) I get such an infection again. I will admit I understood only a bit of what you were talking about as I am not very knowledgeable when it comes to hardware but I would have properly avoided your method for that very reason, I try my best to avoid opening up my computer case and that program freaks me out but again thank you and the advice is appreciated if needed in the future or for anyone else who might need it.

NP, as I said it is a belt and braces approach, it's not as difficult as it sounds, but if your not comfortable going inside a system then it will seem scary, but it's an extremely affective way to clear infections. But as I said above as you've been given the all clear you should be fine with what you have done, but if you get in the habit of right clicking on any files you download, or drives you connect to the system and scan via whatever protection you have available it will help minimise risk, of course you only need to do this if your concerned about the file\drive in question, hopefully you wont have to face this again, glad your sorted anyway.