Restrict values in Territory list

We are exploring the possibility of using Territories to tab our Opportunities (we currently use 3 picklists).  We used a web service to populate our territories (1200+) in Staging.  We will automatically assign territories where possible; however, there remains situations that require the user to select a different territory.  

Our Problem:

One of the requirements is to restrict the user from selecting the top two territory levels.  

Questions:

1. Is there a way to remove our top levels from the Lookup window itself?  This would be ideal and follow standard design protocols by not even offering invalid selections to the user; but we have not seen this ability anywhere.