Uninstalling (removing) BizTalk Server does not remove SQL databases, SQL Server roles, SQL Server Agent jobs, SQL Server Integration Services Packages, SQL Server Analysis Services Databases, the groups that you created during configuration, or any items that you created in Visual Studio .NET. The BizTalk Server directory also preserves any files that you added.

Important: You must remove your BizTalk Server configuration before you delete BizTalk databases. If you do not remove your BizTalk Server configuration before you delete BizTalk databases, the registry keys for the databases are not deleted. For information about removing your BizTalk Server configuration, see Removing the BizTalk Server Configuration.

You can manually delete the following BizTalk Server databases when you remove BizTalk Server:

Or you can use this SQL Server script to delete all the BizTalk Server databases.

 

SQL
Edit|Remove
USE msdb ;   
GO   
 
EXEC sp_delete_job   
    @job_name = N'Backup BizTalk Server (BizTalkMgmtDb)'@delete_unused_schedule=1 ;   
GO   
 
EXEC sp_delete_job   
    @job_name = N'CleanupBTFExpiredEntriesJob_BizTalkMgmtDb'@delete_unused_schedule=1 ;   
GO   
 
...
Note: A number of BizTalk Server-related jobs under SQL Server Enterprise Manager - SQL Server Agent still exists, including also a BAM Analysis database and several SQL Server Integration Services packages, that you also need to remove.

About me

Sandro Pereira
DevScope | MVP & MCTS BizTalk Server 2010
http://sandroaspbiztalkblog.wordpress.com/ | @sandro_asp