All folders in my server look to be comprised, full of files which different names.. I think this took place because the CMS used was not updated.. What do i do now? What can i install on my server to prevent this after updating the CMS ? THANKS
Are the names random like "rzfh82393dafs.php"? In that case hackers have accessed your site. You must delete everything, then install a clean copy from a backup and remove any unsecure plugins you are using.
Sounds like you got hacked. What CMS are you running? WordPress? Typically old/outdated plugins, or 'nulled' premium themes/plugins are to blame. You basically need to back it up and then go through the site with a fine tooth comb. Find the original (safe) sources for plugins/themes/etc and start over.
Unfortunately, you will have to wipe everything clean and start from scratch. You have no way of knowing how the server was infected so the hackers automated systems will be right back. If it is a CMS, then you don't know if they've added additional admin users to the database so just replacing the files will not make your server safe.