You don't have to do this step but I wanted to. I want the bird's body to be solid, so I want to get rid of the outline of the beak within the shape of the body. If you want to do this, follow these steps.
Pull the bird vody to another part of the mat, away from the rest of the file (or you could make a copy and use this first to be sure that you get it right). You will want to weld in a shape that will fill in that space (be careful not to cover up the eyes!). I chose the oval shape from Basic Shapes and find a size that will fill in the roundness without covering the eyes.