What is the structure of an atom?
We can imagine an atom as a small, very dense nucleus, then a large volume of empty space, then a series of regions in which there is a probability of finding electrons. We could represent these regions as 'clouds'.
This is an interesting question, because the answer changes as we learn about more and more complex models of the atom.
The simple one we usually use first is a 'solar system' model, where we imagine the nucleus as being like the sun and the electrons as orbiting it like planets.
As we learn more, we find out that only certain orbits are possible.
Later, from a quantum mechanics perspective, we realise that the electrons exist in regions of different shapes called 'orbitals'. These can be represented as looking like clouds.
All of these pictures are only models that help us to gain a better understanding of what atoms are really like and how they behave.