Which area of the body is microbe-free?

You body is free of microbes inside. That would be inside the cavity that contains the heart, lungs and the outside of the intestines and outside of the reproductive organs. The layers under your skin are germ free. The muscles, bones, blood vessels, heart, brain, spinal cord and nerves are microbe free. All their connective tissues as well.
But every part of your body that has an outside connection is not. That would be the respiratory tract (nose, trachea and lungs). That would include the mouth, inside the stomach, intestines and to the anus. That entire tract is really outside of your body. The same is true for the reproductive organs. The opening and the areas that lead to them can have microbes.
This is rather hard to wrap your mind around this.