It is not normally advised to add soil on top of exposed tree roots as this then cuts off the roots access to oxygen. What you could do however, is bring the dirt up to where the roots start showing at the furthest point from your tree, and then place an organic mulch such as chopped straw, shredded leaves, cocoa beans, or untreated bark mulch around the remainder of the area around the tree. This allows oxygen to still get to the roots of your tree, but fills in that unwanted dip. I would not put the mulch any thicker than 4 inches or so.
Hope this helps!