David Geller. pediatrician. How you clean up during a diaper change depends on how messy it is. If the diaper area is clean, without any stool, then you do not have to wipe the baby's bottom and can just put on a new diaper with or without using diaper cream.If the bottom needs cleaning, you can use a moist washcloth or soft towel with or without soap on it. You may also use wet wipes if you want.avid Geller. pediatrician. How you clean up during a diaper change depends on how messy it is. If the diaper area is clean, without any stool, then you do not have to wipe the baby's bottom and can just put on a new diaper with or without using diaper cream.