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Most of the time the virus are programmed to disable Windows Task Manager, Regedit, command prompt, folder options and etc. These restrictions are meant to prevent a normal computer user from using these built-in Windows diagnostic tools to remove the virus from computer.

There are some virus that will cause destruction such as encrypting recently used files so you are forced to buy the decryption key from the virus programmer. Then there’s another type of virus such as BDS.Mirc.Backdoor that will hide your document files by setting the hidden and system attributes to the file. You can still see the files if you set to show hidden files and folders plus disabling hide operating system files. If the virus is capable of restricting Folder Options, chances are you think that your files has been wiped out by the virus but in fact it is hidden in your system.

Here’s how to show hidden files and folders or system files.
1. Go to Control Panel and open Folder Options.
2. Go to View tab and select “Show hidden files and folders”. Then uncheck “Hide extensions for known file types and Hide protected operating system files”. Do take note that some virus that are still active in computer will revert the changes that you made. So make sure your computer is clean from virus first by scanning with an antivirus program.

3. Try to look for your missing files in your directory or hard disk.
4. This is the method of doing it without using any software. Just run com
mand prompt (Start > Run > CMD), type the command attrib -H -S C:\path\to\your\files. You can also use the asterisk character to define multiple extensions. For example, attrib -H -S C:\nick\*.* would remove the hidden and system attribute of all files in nick folder at C drive.

Others method can refer here

Now if you want remove attrubutes for all files in all folders on whole flashdrive do this:
attrib -r -s -h /S /D
this command will remove attrubutes for all files folders and subfolders:
-read only
-system file
-is hidden
-Processes matching files and all subfolders.
-Processes folders as well