I just take them out whenever I remove babies. I do that about twice a day. First, I raise the humidity inside the incubator as high as it will go. Then I make sure I have a bin for shells and a container for babies right beside the incubator. I open it, quickly but carefully remove all the babies, then quickly gather up the major pieces of shell and toss them in the bin. Close the incubator, put babies in the brooder and shells in the trash. I keep the incubator open less than a minute.