You might notice little brown marks on the surface of the shell and sometimes, on the whites after peeling. That’s a result of the egg touching the pan while baking. You could try cupcake liners or wrapping cotton or foil around the edges of each hole. But if the marks bother you that much, you could get rid of the muffin tin altogether. Alton Brown makes oven-baked eggs with a moist kitchen towel that’s placed directly on the oven rack and the eggs resting on top. That, however, is a serious fire hazard. To play it safe, either rotate the eggs halfway through cooking or slice off the brown bits after cooking and peeling.