An antivirus software will not help you a bit if your server is insecure and has been rooted somehow. On a server, AV software can be used to scan user files for a mail or file server or a web server which supports user file uploads but it offers only very limited protection against the threats a server faces.
If you have malware on it, take it offline, rebuild the server from scratch and secure this time. This means, among other things:
- Learn how it was breached the first time. Fix this hole.
- Keep it updated
- Install as few services on it as possible
- Only install software (especially web related) that is actively maintained and kept updated. This also means not to install every plugin you can get for Wordpress, Typo3, Drupal etc. Many of these suck, security wise.
- Use only secure admin methods (https for plesk, SSH with certificates, no FTP or any other plain text auth)
- Configure a packet filter and maybe something like fail2ban