And what is a "Light Layer"? The only lights AE has are 3D lights and they are just gizmos that don't obscure anything since they don't contain pixel data. You need to explain yourself better.
If you mean a lens flair on a black solid or one of the CC light effects then you can use Screen or Add blend modes to lay the effect on top of another layer if you applied the effect to a black solid.
If you mean you have applied the effect to a black solid and you want to export a clip with an alpha channel then do a Google search for the Red Giant plug-in called Unmult. Apply that and you'll be in good shape.
If you mean something else, please explain.