What is the shape of an atom?

For the purposes of evaluating, discussing and working with them, atoms are almost always treated as if they were spheres. 

However, a sphere suggests that there is a hard and definite line between what "is" and "is not" the atom. We can say that an atom "has the shape of a sphere," but it is not a sphere. This is because the outer layers of the atom, composed entirely of the electron orbitals, are essentially...

For the purposes of evaluating, discussing and working with them, atoms are almost always treated as if they were spheres. 

However, a sphere suggests that there is a hard and definite line between what "is" and "is not" the atom. We can say that an atom "has the shape of a sphere," but it is not a sphere. This is because the outer layers of the atom, composed entirely of the electron orbitals, are essentially like a cloud, with different densities at different times, which we can't precisely predict. For example, if a perfect snapshot of a helium atom was something we could actually acquire, its pair of electrons could not somehow disperse themselves evenly over the entire spherical volume of the atom; they would need to be localized somewhere. So, the spherical shape is an approximation that we make for the sake of convenience and practicality. Some of the exceptions to these conditions lead to phenomena like London dispersion forces or induced dipoles. 

Furthermore, there are considerations we have to make for the differently shaped orbitals that heavier elements are composed of, as well as external forces that can distort the orbitals. So, it's fair to say that atoms can be approximated as spheres, and depicting them as spheres is acceptable in most cases, but we have to acknowledge that they aren't truly "spheres" in the geometric sense, and that this is a generalization.