you would be best to unistall your regular antivirus after this fix, as these malware viruses take over them so they dont search proper, so after malware bytes finishes, and you believe your computer is safe again reinstall your regular antivirus security, thing is also many antivirus software, have trouble finding malware programs as they act the same as regular programs, set your explorer not to allow popups or auto downloads, to help avoid this in the future.
you will still most likely have to change the properties on your files to bring them out of hiding. the virus would have just changed that to hidden.