A conceivable way could be to disrupt the nuclear force of the target atoms, maybe like an anti-Pion/Gluon ray that self-propagates the reaction through the released energy.
(As we might remember, splitting the atom yields a bunch of energy, and uncontrolled such reactions go Hiroshima)
It might be controlled by sub-particle lensing, probably some kind of magnetic field, to be active at a specific distance.
For the reaction to be contained, either there’s a radially limiting component (air is not particle dense enough to propagate the reaction, or atoms not energy dense enough) or it’s a cascade triggered by the beam which stops when the beam stops (or the reaction gets too far away from it)
As I believe Pions and Gluons are their own anti-particles, I don’t know how we would go about doing this, but hey, that’s for Science!™ to solve.
Science fiction is in it’s essence the exploration of a situation when all the confounding factors have been magicked/scienced away.
Not uncommonly it explores the requirements of the technical solution, what would the machine need to do for this to work out? And/or What happens if it doesn’t?
Take for example “Do androids dream of electric sheep” by Philip K Dick, it’s about finding androids advanced enough not to know they’re artificial and how to identify and relate to them when the only diagnostic is slow, clumsy, and suspect. It’s more an exploration of what makes a person than it’s around the marvels of The Machine™.
During the 1900s the vehicle for science to magick with had been machines, computers and AI. Remember that space travel, fission power, psychology, modern medicine were all new, hope inducing breakthroughs just this same period.
There’s also the issue that the definition of the genre came after it becoming large enough to matter. The edges between scifi, punk/cyberpunk, speculative fiction, isekai and even to fantasy are all made after the fact, meaning modern machines go into scifi, old machines go into steam-/diesel-/etc-punk. The main difference between Science, Magick, and Eldritch horror is how detailed the mechanics of the solution are described, and speak to different people.
But on the topic of the story not being centered around a machine: try the Hyperion series by Dan Simmons.
Or go the entirely other way with Ring World by Larry Niven. There’s plenty of machines-did-it in the fringes, but the central theme is to figure out what would be needed for a Ring World to exist, what would happen on it, and how would it be managed. It’s an exploration of physics more than anything - more “what is the machine” than “machines-did-it”.
And the Foundation series (Asimov) famously explore the premise “what if sociology works”, and the other details solved by throwing machines at them.
You also have The Culture (Iain Banks) series that center on/around post-scarcity society and explore that.