From what I understand when physicists speak of energy they are referring to what "stuff has" not an actual thing. So energy would be immaterial I believe.
However the reason I don't buy the illusion idea is because if I take a photo of something, leave it for 20 years and go back in 20 years the photo of what I had taken stays the same even if what had been there has change. So something obviously existed there, something obviously was removed form there. It is hard for me to even fathom this idea that it's all some giant non-substance base illusion. The properties that we perceive may not necessarily be correct (though who is to say what is "correct"), but something is obviously there.
I figure that since energy is just another form of matter then energy is some sort of stuff, that is, it is as much stuff as anything else is including matter. I mentioned mass because in the atom you have various particles and forces, some with mass, some without. Anything "immaterial" in an atom, other than space, would be a product of something material and likely material with some sort of mass.
With our experiments we have mapped out all the atomic particles and there is definitely something there, just at specific frequencies. The immaterial portions of matter would be dependent on the stuff that is there. For example, the higgs boson is giving everything mass and keeping everything from flying a part, and I believe that the higgs boson should count as some sort of stuff or substance. If there were nothing there, there wouldn't be any boson to look for in the first place.
I've heard people talking about virtual particles. Is that supposed to mean it is virtually a particle, almost but not quite? Particles popping in and out of existence doesn't really work for me, there are likely more reasonable explanations, like the boson is always there in the atom but just pops in and out of where we happen to be looking.