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View Thread: Why the need of NTFS as base of SQLServer/WinFS?
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    As far as I know, you 'can' configure SQL Server to use raw disk partitions (see Using Raw Partition in SQL Server Books Online). I don't know how far this goes, as I have never had to configure a system this way.

    In the case of WinFS, I think the DataBase will not hold the files per se, just metadata to perform searching and cataloging. The files reside on NTFS partitions.