Inner loops and extruding!

I have created these cut out stencils of sycamore trees within a statement window both using the same model to extrude these holes. However in one some of the geometry remains, I assume this is due to hidden inner loops. But I am not too sure how to resolve this issue! I know it is a tiny imperfection but the inner perfectionist in me cant allow it!

I’m not completely sure how you want this to work, but I have cleaned it up for you.
I basically cut the panel down to a single face and used intersect faces with selection a couple of times to make the edges cut, while removing all the extra edges. Then redid the thickness and inset the sycamore panel.

sycamore tree sketchup FINALBox.skp (783.2 KB)