I think part of your problem is psychology. You use the word "remove". I don't think you can look at this way and the brain can certainly aid or hamper healing. You can't remove them, you can only help the body heal over time since they are just areas of incomplete healing.

Deep/large scars will fester forever on a human that is never able to purify their blood to the point where damage repair can truly begin. Fasting is the only method I know of to achieve this, and in the case of deep scars you have to get DRASTIC. Before you kill yourself, why not try a series of lengthy fasts? Since you eat well already you probably have pretty good mineral reserves.

Keep at it, it will take time. But at some point you may have to accept what your body gives you. We all have our problems and limitations.