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Not sure what you mean by "cleaning up" the database. Exchange does the clean up for you during the nightly maintenance interval, and you normally don't need to do any cleanup manually. Besides, such clean up, or offline defragmentation, will result in an outage.
Nevertheless, should you want to do this, the first step is taking a look at Event ID 1221 in the server's Application Event Log for that store. it will tell you whether there is enough free space in the store. If there isn't much free space, I wouldn't recommend doing it.
If you've determined there's enough free space in the store and you need to reclaim disk space, the command is:
eseutil /d
Other details and considerations for offline defragmentation are documented in KBA 192185.
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