The good news is that partition alignment is simple to perform; the bad news is that partition alignment must be done at partition creation time, prior to partitions being formatted. This is great if you have a new SAN, but it might be painful to convert large amounts of existing data on misaligned partitions.
Caution: Realigning partitions using any tool is a destructive operation, because it wipes out existing data.
Here is a template for using diskpart.exe to perform partition alignment, assign a drive letter, and format a partition.
Diskpart
list disk
select disk create partition primary align= assign letter= format fs=ntfs unit=64K label="
