I guess this Map object you are referring to is a custom class you made? A tile map is just an array (generally a 2d grid but can be 3d of course). If you update your Map object to have an array and populate the array with the corresponding GameObjects from your prefabs you will gain dynamic control over them. Being able to add and remove GameObjects at runtime.
If you show some screenshots of what you are currently doing and show the code for this Map object you mentioned that will help a lot to get a better answer.