The shape of hydrogen (and all atoms) is made up by the way the electron spreads itself, as a wave function. This wave function is a blobby shape, and often looks like spheres and donuts put next to one another. The wave function is the electron itself, in a sense. When you don't disturb it, the electron looks like that. When you do disturb it, it becomes a single hard point, and the blobby shape vanishes.