The list of addresses you can be send or recieve from at is what is associated with your Apple ID. You can manage them at:
https://appleid.apple.com/cgi-bin/WebObjects/MyAppleId.woa/wa/directToSignIn?loc alang=en_US
You can also get to the apple ID site by System Preferences/iCloud/Account Details/Manage Apple ID.
You can uncheck the ones you don't wish to use in the preferences of Messages, but to remove them from, you need to log into the Manage Apple ID website and remove those addresses there. That is where the email addresses used in Facetime, Messages, or anything Apple are stored. It doesn't delete the addresses, but just removes the ones you don't want associated with those apps.
You can also change or remove any non Apple (iCloud) email address associated with your Apple ID at this website.
A second way to remove addresses from Facetime & iMessage is within Facetime preferences. In the Facetime list, click on the circled > to the right of the address and you have an option to remove it there. It will also remove it from iMessages. I don't know why Apple has left this option of removing addresses out of iMessage. It does allow you to add an address though.
You can also go to iCloud.com to manage which Apple email addresses you want to send mail from, but it won't prevent you from recieving mail from all iCloud addresses you have.
For more detailed info on Apple ID and uses:
http://www.apple.com/support/appleid/