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It is not directly possible by Setup feature but you may create few custom fields to manually select from a list if that fits your requirement.
See the association of Custom Object to teritory using APEX in the article below,
http://blogs.developerforce.com/engineering/2013/03/salesforce-territory-management-and-programmatic-sharing.html
Also see the discussion in the below link,
https://success.salesforce.com/answers?id=90630000000gkbOAAQ
Regards,
Ashish