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Apparently disk performance is much improved if you do this. Make sure you do this for each new physical disk. Procede as follows –

1. If the disk you are aligning is already blank (raw), proceed to Step 3. If the disk contains data, back up the disk before proceeding.
2. Delete all partitions on the disk.
3. Open a Command Prompt window, and run Diskpart.exe.
4. At the Diskpart command prompt, type List Disk and press ENTER. If the disk you want to align does not appear in the list, make sure that it exists and is accessible using the Disk Management snap-in.
5. At the Diskpart command prompt, type Select Disk X, where X is the number of the disk as shown in the output of the List Disk command. Diskpart should return a message that indicates that Disk X is the selected disk.
6. At the Diskpart command prompt, type Create Partition Primary Align=X, where X is the value recommended by your storage vendor. If your storage vendor does not have any specific recommendations, we recommend that you use 64.
7. At the Diskpart command prompt, type Assign Letter=<DriveLetter>.
8. After the drive letter is assigned, type exit to exit the Diskpart tool.
9. Use the Disk Management snap-in or the Format command to format the partition as an NTFS-formatted partition.

The link to the MS technet article is –

http://technet.microsoft.com/en-us/library/aa998219.aspx