some people say that it is not a good idea to do a file-system defrag on an exchange server. Now the file-system defrag is different than defragging the exchange databases themselves which is a good idea and can be scheduled to run on the exchange server with the built in defragmentation tool. there is also the offline eseutil.exe utility, but the system has to be offline to do this. Please read the following article:
And this article from MS:
In this case, it would better if you will use a third party utility defragmentation software to effectively defrag your hard disk drive. However, most modifications of defragging a hard disk drive are available only on a licensed software so you may need to purchase the software.