What do you do with stones in harvest moon magical melody?

Nothing. In Magical Melody, stones have no purpose except to be a nuisance. They may block your path or be inconveniently placed in the middle of your fields, so break them with your hammer just to get rid of them.

that is not true

Instead of using wood to make fence to the animals you can use stones

then you can use the wood for other things a windmill or a barn

i love the stones