You can remove configuration settings from a BizTalk Server without uninstalling the BizTalk by opening a command prompt and executing:
configframework.exe /u
Confirm the configuration has been removed by launching BizTalk Administrator. The application will notify you of the lack of configuration on startup. This is useful if you are changing the role of an existing BizTalk server in an organization.
Note: this only removes the configuration settings from the server. It does not remove SQL databases, SQL maintenance, OLAP cubes, users or groups. By itself, this does not restore the server to a vanilla state. If your intent is to do this, please see “Restoring a BizTalk Server to a Vanilla State”.