Ubuntu – Remove RECYCLER directory from virus infected flash drive

Before you advise me on the option of saving my files and formatting the drive using gparted, please understand that I could have done that hours back and that would have taken only a few minutes. Actually, I want to understand, what is really happening here. The situation is trashing all my experiences gained over the years.

I was under the impression that if I insert a virus infected flash drive to my Ubuntu machine, all I need to do is to simply delete the virus files and I am good to go.

Today, I collected some files in an NTFS formatted flash drive from a Windows machine fully knowing that the machine is virus infected. When I inserted the flash drive to my machine, I found that indeed, it has collected many files and folders. I have deleted most of them. The only one showing hard resistance is a RECYCLER directory (and its subdirectories).

The attributes of this directory.

drwx------ 1 masroor masroor 4.0K May  7 16:01 RECYCLER/

If I execute the rm command,

sudo rm -rvf RECYCLER/

I get a long output in the line of,

rm: cannot remove `RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/OagFrAIX.exe': Input/output error
rm: cannot remove `RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/viJbcvrJ.cpl': Input/output error
<rest snipped>

What is interesting, the above reported files are shown by the ls command with some
myriad set of attributes.

ls -l RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/

ls: cannot access RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/OagFrAIX.exe: Input/output error
ls: cannot access RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/viJbcvrJ.cpl: Input/output error
total 0
-????????? ? ? ? ?            ? OagFrAIX.exe
-????????? ? ? ? ?            ? viJbcvrJ.cpl

If try to find the attributes of those offending folders,

ls -dl RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/

I get,

drwx------ 1 masroor masroor 4096 May  7 15:58 RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/

Command chmod to make the RECYCLER folder world writable fails.

sudo chmod -vR ugo+w RECYCLER/

The output is in the line of.

mode of `RECYCLER/' changed from 0700 (rwx------) to 0722 (rwx-w--w-)
mode of `RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537' changed from 0700 (rwx------) to 0722 (rwx-w--w-)
chmod: cannot access `RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/OagFrAIX.exe': Input/output error
<snipped>

These folders contained a number of .exe and other files most of which I have already deleted successfully (except the above reported ones).

If I check the attributes of one of these folders,

lsattr -ad RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/

I get

lsattr: Inappropriate ioctl for device While reading flags on RECYCLER/S-2-4-27-3777257131-1806073332-421880436-8537/

I have run clamtk on this device as suggested here. However, it fails to find a threat.

I understand that I can simply save my flash drive contents somewhere and then format it. However, I am more interested in finding out which attributes have been set in these folders which are resisting further changes. (And definitely, I will want to disinfect my flash drive as well.)

UPDATE 1

Further to the comment from Patro.

1. When the folders are visited, those files with myriad attributes are not shown, even when I try to view them as hidden files.
2. Deleting these files fails. The command rm -rvf * inside the directory S-2-4-27-3777257131-1806073332-421880436-8537 fails with input/output error.

UPDATE 2

After the comments from soulsource and girardengo I have tried to run
ntfsck and ntfsfix. Also, this question helped.

Here are the outputs.

ntfsck

sudo ntfsck  /dev/sdc1

Unsupported: replay_log()
Unsupported: check_volume()
Checking 7796 MFT records.
Unsupported cases found.

ntfsfix

sudo ntfsfix -d /dev/sdc1

Mounting volume... OK
Processing of $MFT and $MFTMirr completed successfully.
NTFS volume version is 3.1.
NTFS partition /dev/sdc1 was processed successfully.

But the initial situation still persists. There has not been any improvement.

UPDATE 3 (SOLVED)

As advised in this post, I inserted my drive in a Windows machine and
executed (from a terminal),

chkdsk <drive letter> /R

There was a flurry of activities about checking and repairing. There were some messages regarding bad sectors as well. The task
was finished in less than a minute.
Then I found that some new folders have been created for recovered areas.

I reinserted the flash drive to a Linux machine, and the RECYCLER folder could be deleted without any problem.

As an added step, now I have formatted the drive (using gparted, to NTFS) since I think that I have gained my insight.

Looks like the virus is indeed capable of causing (temporary/soft) hardware
problem. Please see the above mentioned post for a detailed technical explanation.