Yes, this is entirely possible.
People once thought that atoms were the smallest possible unit of matter.
They were wrong.
We now know that sub-atomic particles exist: quarks, muons, leptons, and so forth.
With our current technology level, we are unable to determine if there are yet smaller units or not. We have even theorized that there are, in string theory.
By using a different paradigm of thought, we can reach a great understanding of what we call science from a totally different point of view.
One such example in today's world is the divide between Eastern and Western approaches to medicine. Western science remains unable to account for some provable, repeatable treatments and methods of reaching a diagnosis used in Eastern medicine. This doesn't stop them from actually working.
Another example is how physics once proved that bumblebees can't fly. Yet they do. And eventually they found out that their wings become flexible at high speeds, which they never thought to test or account for and this threw off all their equations and assumptions.
After all, once upon a time nobody thought something could be in two places at once (super-positioning), or be able to talk across great distances (telephone), or see things happening on the other side of the world as it happened (live TV), or teleport (we have now teleported atoms), or fly (the Chinese put a man in the sky via a giant kite looking before the Wright brothers)... I could go on.
By approaching matter/energy theory from a viewpoint of overlapping fields of biased energy types, one can essentially replicate all of our modern advancements without ever admitting the existence of atoms.
After all, all atoms are is a collection of measurable and non-measurable qualities which overlap and interact with each other grouped proximally in a local space time matrix. In other words... an energy field in a constant state of flux, containing a multitude of varying densities, reactivity, and permeability. It is simply convenient and easy to think of them as discreet objects, even though they actually aren't.
Today's physics are already exploring this concept: do a few searches about the holographic universe concept to see some of what I'm referring to.