How do we know what the earth made of?
The Earth as we know it is crafted out of rock.
We know this because many minerals such as gold, diamonds, metals etc. Are alljust refered to as different peaces of rock (different types of rock)
Plants are just life that grows on the plantet and gasses/fluids, well we can't reall walk on or build with gass and/or fluids now can we?
As far as the deepest hole goes, it has all just been rock, wether there is something different below is unknown. And with our current technology it is not possible to find out.