In general I am trying to minimize cost. I know that one option is to roll over and believe that the best time to do this is 2nd Thursday in the expiration month, however I am happy with my future position and its profitable can I not just let it run to expiration and what happens afterwards (what are the mechanics, clearing procedure)?

I suggest you check the costs associated with settlement with your broker so you don't get any nasty surprises. You can let it expire in which case you'll be settled into cash based on the Special Opening Quotation (SOQ) on expiration Friday. Check CME for details.