How do I clean up virus induced hidden files and disabled everything?

Solution 1:

For the hidden files: run ATTRIB -h c:\*.* /s /d. It won't reset system files though. I would then run Malwarebytes AntiMalware to get the task manager, desktop and other security settings working properly again

Solution 2:

Under step 19 from cleaning the "System Fix" infection (which is one that hides everything) from Bleeping Computer:

19.This infection family will also hide all the files on your computer from being seen. To make your files visible again, please download the following program to your desktop:

Unhide.exe

Once the program has been downloaded, double-click on the Unhide.exe icon on your desktop and allow the program to run. This program will remove the +H, or hidden, attribute from all the files on your hard drives. If there are any files that were purposely hidden by you, you will need to hide them again after this tool is run.

I've used it and it worked as expected.

Here's a direct link to the Unhide.exe download, ensure that ALL infections/rootkits are removed first, or it maybe prevented from running. :)