Linux Server tuning

Hi, we have to linux machine equipped with webmin and ispconfig. On once we have webserver with all sites hosted and we have also the mail server activated on another we have just the mail server but we use apache for the webmail. We are having some spam attack and we need a finalization and a tuning from an expert to understand if inside the web servers there are maliciose scripts. We need to protect both the server from those events and we need also a good strategy to keep saftely both the servers. The expert will work remotly connecting directly on our workstation and we keep in contact using IM. Thanks