sambogrub said:
So then why can't I see through my arm? Or pass through another object? Is it the energies interacting with each other?
You're on the right track!
Imagine a pair of magnets with like poles facing each other. The space between them can be empty(in vacuum), yet they'll resist being brought together.
This space is only empty in so far as being devoid of massive particles, but it is filled with fields of various forces, with varying strengths.
From far away, the magnets are "unaware" of each other, but if you bring them close enough, the interaction will become noticeable, getting ever stronger as the distance decreases.
Atoms and molecules(bound collections of the former) act like a multitude of tiny magnets, whose fields collectivelly act to repel(or attract!) other atoms. In their case, it's not magnetic, but electric interaction(both being two facets of one fundamental, electromagnetic force).
When atoms attract, they tend to bind into more complex molecules, which is what chemistry is all about.
As for light, it only cares about the extent of the electromagnetically interacting "stuff" - i.e., the fuzzy cloud of electrons surrounding atoms/molecules. This is because light is the excitation of electromagnetic field.
It doesn't matter how much of the volume of an atom/molecule is occupied by mass, just what is the extent of the electron cloud.
As a rule of thumb, only light of wavelength comparable to the object it hits gets to interact, other wavelengths passing through.
Molecules are about the right size to interact with what we call the visible spectrum(360-720nm, iirc).
Particles that don't interact electromagnetically(like neutrinos) can pass through atoms as if they weren't there.