is this smart to burn fat while also building muscle?

I would say I am low body fat but I am trying to get rid of the last bit. my diet is 90% clean right now and I want to clean it up once and for all so I do not need advice on that. I weight train 5 to 6 days and week and every other day ill run a mile as fast as I can which is about a 5:50 mile. does doing this mile run at the end of my workout burn fat or is it just taking from my muscles? any other cardio I can do to burn the last bit of fat without my muscle being eaten away?