This is freeware, www.PartitionWizard.com .
I used this on a Samsung SSD 256GB drive which had my OS Windows 7 installed on it.
In case things went wrong I had done a backup of Windows 7 using Acronis True Image 2013.
Once I had selected the option to Align Partition the utility exits Windows and reboots.
Oddly once started in a DOS screen I noticed the partition being created was LBA 2048 but the size of the 256GB drive was being partitioned as 164500MB (160 GB).
After about 30 minutes the system rebooted and there were no problems apart from the partition size.
This was corrected using the Disk Management in Control Panel to extend the volume into the unallocated space as below.
After the first shutdown and restart the Chkdsk ran and corrected some orphaned entries.
Western Digital also has an alignment utility but only WD drives can be selected.
Paragon Alignment Tool v4.0 is available for purchase but since Windows 8.1 returns an error message on reboot " Stub Library wasn't initiated" and then opens back up in Windows 8.1 without running the disk alignment but reporting it is completed..
Oddly Aconis Disk Director 11 Home had no alignment option. A suggestion within Acronis Help said that just creating an image and recovering that image would resolve alignment issues but this did not work. The Partition was still not aligned after doing this.
Also many forums say that if you install Windows from any version after XP it is always aligned.
This was not the case on 2 PC's out of 5 that are on my Home Network which were installed from DVD Disk. There is a case for checking and running an alignment tool.