Shared Hosting Server Security Tool against Anti-Malware

I am running shared hosting services running on Windows 2012 R2. Recently faced some security issues on the server where in some websites malicious files & folder placed by hackers. These are my personal websites so I am 100% sure that non of us placed such files on the server.
I ran anti virus but no file is effected. Checked system logging but unable to get any clue. Is there any other tool that could assist checking my server security integrity ?
Thank you