If you're using cPanel control panel, your host provider may provide you a "Virus Scanner" that's ready to use to scan Mail, Home Directory, Web Space, and FTP Space. The name is ClamAV, that will be "Virus Scanner" under Advanced feature group on your control panel. You may contact your host provider to enable it if you couldn't find it.

Aside from having a Virus Scanner help scanning, and uninstalling or fixing those infected ones, the password is the key. Be sure to have one that very strong and complicated enough that only you could remember, update frequently would be more helpful.