When considering light and matter, there is a particular probability that a photon will interact with an atom. This can be thought of as a cross-sectional area of the molecule which interacts with light. Although spatially we like to think of nuclei and electron clouds, when it comes to electrodynamics each atom can actually be thought of as a “solid” cloud of charge. Since the electromagnetic force (transmitted by light) is so strong, it’s reasonable to think of matter as charge components much more than spatial components.
Modern chemistry and quantum mechanics agree that the observed configurations of matter depend primarily on the distribution of charge in the nuclei and electron wave functions (orbitals). The spatial arrangement of electrons can be calculated as a probability, but the charge and symmetry character of the atom is a much better description of its existence (can be calculated exactly).
Although spatially we can think of our bodies and all matter as mostly space (ie, nothing), it’s also true that all matter continuously influences the space around it with an electric field which interacts with other matter (through chemical bonds) and with light (through energy transitions and scattering).