Tree - Too Deep in the Ground
Trees too deep in the ground, an all to common problem, have two basic problems. When the trunk flare in under ground, it stays moist and doesn't breathe properly as bark is supposed to do. The soil too high on the trunk also often hides circling and girdling roots which choke the tree and drastically slow down growth. Trees grown in containers are highly subject to this damaging condition. The simple answer is that it needs to be done VERY carefully.
If you do the soil removal yourself, use hand tools and gloved hands being extremely careful not to damage the wet bark tissue. Water can be used but only with a soft flowing stream. Strong water blasts can severely damage the soft bark on the base of the trees.
By far the best route is to hire an arborist that uses the air spade. It is a fancy sandblasting type tool that blows air (no sand) at a high velocity and removes the soil without damaging even the smallest roots.
Once exposed, the small roots trying to grow up to get air should be removed and the depression caused by the trunk/root flare exposure should be left open. As the flare expands from the growth of a more vigorous tree, the open dish will fill in. All I would put in the depression is a thin layer of shredded cedar mulch.