DiskPart is a utility that, among other things, allows you to specify the cylinder alignment of hard drives. Exchange and SQL particularly benefit from a 64KB sectors. So much so, in fact, that 64KB alignment is (finally!) the default in Windows Server 2008.
There are plenty of resources on the net that explain when and how to use it. A good explanation by the Exchange Blog can be read here and the Microsoft reference for DiskPart is here.
The commands I use are:
Copyright (C) 1999-2001 Microsoft Corporation.
On computer: Exchange2003
DISKPART> select disk 1
Disk 1 is now the selected disk.
DISKPART> create partition primary align=64
DiskPart succeeded in creating the specified partition.
Then open Disk Management, assign a drive letter to the new drive and format it as usual.