virus that turned your folders into .lnk (shortcut)

The virus you’re talking acts by installing itself in your external drive, hiding your folders as system protected files and then creating false folders with the exact same icon and name which serve as shortcuts to the virus itself. As you say you already removed it, all you have to do is change your folders back to a normal state. Here’s how you do it 
(assuming you’re using Windows):
open command prompt 
Simply go to your drive - and  
"attrib -s -h -r *.* /s /d
you will see the [ ] << folder just rename 

and walaaaa your file will show as before