Atoms appear as spheres. Depending on the model, bonds are represented as either fused spheres or by sticks. Please remember that these models are only a simplified representation of reality. The emphasis is placed on spacial relationships i.e. bond angles, orientation, and size. The similarities between models and reality end there.
Electrons are many magnitudes smaller than the nucleus.
Take the hydrogen atom as an example. Hydrogen possesses one proton and one electron. The radius of a proton is approximately 10 to an exponent of -15 meters. An electron, however, does not occupy a measurable volume of space. It has wave and particle like properties.