amirali1928,
Regardless of whether you scanned you USB flash drive from the Avast "scan" in the Windows Explorer right click menu, or from the "Folders" scan in the Avast Simple User Interface, the result should have been that when it found a file with a virus, it should have put up the virus warning and offered you the choice of Move/Rename, Delete, Move to chest. If you selected Move to chest, it should have done just that, and the file on the USB drive should have been "deleted".
So if there were large numbers of files found on the USB flash drive with infections and these were moved to the Chest, when you next looked at what was on the USB drive, it should have contained only those items which were not infected, and in tests I have run using a USB 560MB flash drive (memory stick) with EICAR virus test files on it, thats exactly what occurred.
Now on the flash drive I used on my tests, the files "moved" to the Chest on the hard drive were no longer visible at all on the USB drive using Windows Explorer, nor did Avast show them at all on subsequent scans of the USB drive, so I don't know why you can see them greyed out.
On a normal hard drive, a simple delete doesn't really delete a file, but just alters the drive table so it is no longer visible. I am not sure whether avast uses a more secure wipe process to overwrite the data in the original infected file before it "deletes" it, but I believe even wipe processes are not always completely effective on USB flash drives because of an internal hardware feature implemented to stop sections of the flash memory from being excessively used, so perhaps the hardware in the particular flash drive you have is still allowing you (and avast) to see the drive table entry for the original files, greyed out and not able to be accessed - but that's still pretty odd.
A copy of the infected files should still be in the Chest, and you could restore them to the flash drive, but that would be most unwise as they would still be infected and without putting a noose around you neck and turning off avast, you still wouldn't be able to open them. Rescanning them with another antivirus scanner would perhaps give you an idea of whether any of the files nominated by Avast as infected were just false positives, but that is unlikely to be the case for such large numbers of files.