Some malware will hide files, especially when you insert a removable device such as flash memory, external hard disk, etc. In most cases, your files are marked as system and hidden files and by default they are invisible unless you change the folder options to show hidden files and system hidden files. You could make those files visible by removing their system and hidden attributes. In order to recover your hidden files you could follow these steps:

1)      Run a scan on the infected device to make sure all malware has been removed. You could use Microsoft Safety Scanner and click on custom and select the driver of your infected device and run a scan.  

2)      Open Notepad. To do so, open Start, search for Notepad and open it.

3)      Inside Notepad, write this text:

         attrib –s -h

4)      Save the Notepad file as unhide.bat (Note: it could be any name but the extension must be .bat so it is DOS batch file <name>.bat)

5)      Copy and paste this file in the place that you want to unhide your files. Run it and it will unhide your files. If the file didn’t unhide your files, you might try right-clicking on it and choosing Run as administrator.

6)      You can remove this file later on.

IMPORTANT: The process above will remove system attributes and if there are system files they might become visible. It is recommended to only use this method in removable storage and external devices and not inside Windows and system folders.