Apply several coats of polyurethane in the recessed areas, using a small brush.
It will take you an obscene amount of time because you will have to wait for it to cure between coats. You will need to sand it back some between coats. Then when you are done, you will have to sand some of it to match the surface transition over the gaps. The final result should look good, though: it will have a transparent, epoxy-like finish.
This is a good example of why the unevenness should be addressed before applying the finish, much like how you want to put body filler on panels and sand them smooth before applying the paint, because paint does not fill holes very well (too thin).
Keep in mind that around the longer gaps, the height of the surface on either side of the gap might not be the same. Use a straightedge to quickly check for flatness across the gap.
Alternately, you can sand off some of the finish in the gaps and fill with colored epoxy or plain wood filler. You will not have to put as many coats to achieve desired flatness.