Here is a brief quote on how to optimize the NTFS performance from http://msdn.microsoft.com/en-us/library/cc949109(v=sql.100).aspx
Optimizing NTFS Performance
By default, NTFS is not configured to handle a high-performance workload with tens of thousands of files in an individual file system directory (i.e., the FILESTREAM scenario). There are two NTFS options that need to be configured to facilitate FILESTREAM performance. It is especially important to set these options correctly prior to undertaking any performance benchmarking; otherwise, results will not be representative of true FILESTREAM performance.
The first configuration option is to disable the generation of 8.3 names when new files are created (or renamed). This process generates a secondary name for each file that is only for backward compatibility with 16-bit applications. The algorithm generates a new 8.3 name and then has to scan through all existing 8.3 file names in the directory to ensure the new name is unique. As the number of files in the directory grows large (generally above 300,000), this process takes longer and longer. The time to create a file in turn rises and performance decreases, so turning off this process can significantly increase performance. To turn off this process, type the following at a command prompt and then restart the computer:
fsutil behavior set disable8dot3 1
Note: This option disables the generation of 8.3 names on all NTFS volumes on the server. If any volumes are being used by 16-bit applications, they may experience issues after you change this behavior.
The second option to turn off is updating the last access time for a file when it is accessed. If the workload briefly accesses many files, then a disproportionate amount of time is spent simply updating the last access time for each file. Turning off this option can also significantly increase performance. To turn off this process, type the following at a command prompt and then restart the computer:
fsutil behavior set disablelastaccess 1