When you shine a light on a 3D layer, you can make the light pass through it just like sunlight passing through a stained-glass window. The light casts a shadow on any layers behind the stained-glass layer, and the shadow's color and shape will be taken from the layer it passes through.
Remember to enable shadows for the light layer.
Then twirl open the stained-glass layer's Material Options. Turn Cast Shadows on and set Pass Through to 100 percent.