I only had two mediums for brood, but yes, I removed the mediums as they were vacated of brood. Usually the bottom medium, if you run three, will not have any brood in it at all at this time of year, so you could remove that one right away, but check it first for brood. A deep added on top of the stack will occupy the queen for quite some time with her laying, enough time for all the brood in the lower boxes to hatch out and for you to remove them. But you will have to monitor them closely so she doesn't go back down and start laying in them again. Even if you find only eggs in the mediums when you go to remove them, its no big deal, eggs aren't expensive.