Tenable's research group today released a check for Nessus which discovers systems not-running NTFS file systems. For example, a system running on top of FAT32 would be detected by this plugin. The plugin is named "Insecure Logic Drive FileSystem" and has a Nessus ID of 24871.
If you have a Windows Server system not utilizing NTFS, then there is very little security offered at the file level. NTFS offers the ability to set permissions on user files and folders and also makes it more difficult to gain access to system files.
The check considers every file system on the remote Windows server, not just those being shared over SMB.
This check is accomplished through Nessus 3 Windows WMI queries and is currently available to Nessus Direct Feed and Security Center subscribers. Tenable releases many Nessus plugins each day and offers this RSS feed for users and customers to remain informed.