Checklist: Undeploy a BizTalk Application
Delete the BizTalk application from the BizTalk group. This removes it from the BizTalk Administration console and the BizTalk Server databases.
Uninstall the application from any computers on which it has been installed.
If necessary, remove the assemblies that were included in the application from the global assembly cache (GAC).
Remove other files and settings from the local computer that were not automatically removed in the previous steps.