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You can defrag:
There are two things to consider when you want to do a file defragmentation of your drives:
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Never try to defrag your Exchange databases using a program like Diskeeper. Those are normally placed in C:\Program Files\Exchsrvr\MDBDATA directory. If you have moved them to another location you should excluded this folder in your favorite defragmentation software.
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Never try to defrag the M: drive using a program like Diskeeper. Exclude the M: drive in your favorite defragmentation software
If you have deleted a lot of email messages or other stuff that is stored in Exchange you can do an offline defrag of the Exchange databases using the esutil tool from the Exchange bin folder. More information on how to use eseutil: 192185 - XADM How to Defragment with the Eseutil Utility (Eseutil.exe)
Before you can do an offline defrag of your Mailbox Store and Public Folder Store. In the picture below I dismount the Mailbox Store. If you do this when users are connected to Exchange they will loose the connection and maybe even data. An offline defrag can take from several minutes to several hours or even a day. I once did a defrag of a 36 Gb Mailstore and that took more then 13 hours to complete! A defrag of the stores with eseutil defrags the internal file structure of the stores and will shrink the total 'on disk size' of the stores when you have deleted many items in Outlook. It does not do a file based defrag.

In the C:\Program Files\Exchsrvr\MDBDATA you will see a lot of files:

The file you will defrag with eseutil are priv1.edb and pub1.edb. If you type eseutil /? you will get an explanation of the several command line options. For a defrag I choose eseutil /d priv1.mdb. Below you see a picture with the eseutil output after running the command.

Before the users can use Outlook and connect to Exchange you have to mount the store(s) again:

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