Forum Moderators: phranque
As we do not know what kind of server you on and how the hackers were able to enter your system in the first place, it is difficult to give any directions. The best way would be to solve this together with your hosting company, as they might have experience with this specific type of hacking of your server.
Are you on shared hosting, a virtual private server or a dedicated server? If on shared hosting, it could be that the attack is not from the outside, but from one of the other users hosted on the same server.