How to prepare mushrooms When you make stuffed mushrooms, the key is to carefully remove the stems from the bottom. First, you should use cool water to rinse off the debris and dirt from the mushrooms themselves. Once you have the dirt off, you can use a spoon or knife to carefully remove the stem from the bottom of the mushrooms. The underside of the mushroom cap should have a bit of a cavity to it. You don’t want to dig into it too much because you may break the cap, which will make it impossible to use the cap for the recipe.