I use Ubuntu 9.04 exclusively on my own machines, but I have a couple of flash drives that got infected by some corrupt windows executable (*.exe) files, probably by somebody's trojan (they are Cruzer 4GB so came with installed fancy programs that I dont need but didnt remove and Windows keeps installing unwanted ini files and other trash every time I use them in somebody elses machine or in an internet cafe). I deleted quite a few files, but some are stubborn.
$ sudo chmod +w-X doesnt seem to work. How do I unprotect and remove them? The filesystem is vFAT.

I suspect the files were created by some kind of a trojan as my work requires my flash to be pretty promiscuous.
When I 've backed up all the good files I need, I'd be happy to reformat the flash drives as straight vanilla data storage and retrieval, provided I can still use them on a variety of machines running MS windows as well as on my Linux machines. Any guidance on reformatting?

Cruzer?? Not the U3 junk, is it? Because if so, the ONLY way to get rid of it is to use the U3 uninstaller, which you have to download from their website, which is Windows only. Otherwise, NOTHING will get rid of it.

If you mean other stuff than the U3 software, you could do a "sudo chmod -R 777 *" on that device, and see what you can delete then, but that may not work either. A reformat may be the best and quickest option.

Should be easily done. The device is probably /dev/sd* (a guess would be /dev/sdb, since your HDD is probably /dev/sda, but check first). So, unmount the stick first, but leave it plugged in. Then, run "sudo fdisk /dev/sdb" (obviously, replace the sdb with your device name). Delete the partition(s) on it, and create a new one....the fdisk help is simple to follow. After that, you can do "sudo mkfs -t vfat /dev/sdb1". That should create you a 'portable' Windows/Linux stick, ready to go.

Thanks. It was U3 junk. I backed up and reformatted, and used the partition editor (gparted) instead of the command line. It seems to work pretty well.