Eagle PCB design issue
Your polygon pour is filling in (showing as blue). To make your "background black" under the transformer, you need to change the shape of your polygon. When you created the polygon, you had to first draw the outline. All you have to do is click the outside edge of the pour and it should highlight the edges of the whole polygon. You can then drag the sides to change its shape.

Not sure why you don't want the pour under the transformer though. Assuming it's insulated with solder mask and your transformer is in a protective case, having the polygon pour completely shouldn't be a problem.