Many people face the issue of shortcut virus from the pen drive or any other portable drive. The symptom of this virus is every folder you have in your USB drive will be converted to shortcut icon and if you double click the shortcut, it will open the same folder in a new window.
Symptoms of shortcut virus in Pen Drive
In the beginning I was not so serious about the issue until I faced the same myself. If you search in Google for the solution of pen drive shortcut virus, you will see a lot of sites which has given almost the same sort of solution. Almost everyone shared a batch file throughout the google search that I came across. The batch file simply does 3 things-
1. Unhide all the files in the USB drive.
2. Delete all the shortcuts in the USB drive
3. Delete two files called fypuas.exe and fypuasx.exe.
You need to know that by this solution the issue is not resolving permanently, and it will only last until the computer is restarted. If you insert your USB drive after restarting the computer/laptop again, it will show the same issue which I have discussed above.
Permanent Solution of Removing Shortcut Virus from Any USB Drive
Let me give you a brief overview of what this virus does before getting started to walk on the steps to delete this virus from your USB drive. It makes easier for you to understand and see the solution of the problem.
Shortcut virus surfaced in 2010 and gone through with different names since that time. It injects itself to system startup, makes a few self-executable files inside the USB drive which look like shortcuts which hides the original folders and files inside the USB drive, replicate itself into the profile folder of the user. The right clicking of any shortcut folder, inside your USB drive and going to Properties, anyone can able to confirm that this is not actually the shortcut but properties of an executable file.
So, lets move on the walkway by which you can remove the virus from your USB drive step by step:
1. Go to Run (widows key + R) and type %temp% and hit Enter.

2. A window will appear, and you will see many unknown files and folder in there.
3. Select all and permanently delete.
4. Again, Go to Run (widows key + R) and type prefetch and hit Enter.

5. Another window will appear and select all and permanently delete.
Now you are free from cache which can act with USB drive shortcut virus. Just follow the below steps now to remove the virus from USB drive and restore all the previous files and folders those were in drive before:
1. Go to Run (widows key + R) and type cmd and hit Enter.
2. Run the following command: attrib -h -r -s /s /d E:*.* (Just go to My Computer/This PC to check what drive letter holds your USB drive. Here my USB drive denotes letter E, I’ll need to type E: and hit the enter key. This will take you to the USB drive inside the command prompt)

This cmd command will erase the following attributes which was present in files as hidden and read only inside the USB drive.
By following the above steps, you should be able to remove the virus from the USB drive completely. Not only remove the virus, but also the above command will also restore your files and folders which were in that drive before the cation.
Now, if you open your USB drive, you will be able to see all your files and folders restored inside the USB drive.