hmm, i was always under the impression that fs's body was actually akin to a fusion reactor.... not sure his biology is the same as a normal person, or hero. if his body is too harsh of an environment for atom to enter or survive in, he has no chance at all. if he can handle being inside fs (no homo) then he might be able to take him out like he could take out most by causing internal damage to something vital. not sure if fs could detect atom inside himself. if he can, atom would need to work very quickly.
seems iffy atom would stand much of a chance here to me, at least at first glance.
Well I do know that Firestorm can see Atom when he's in the subatomic realm, and even force him to withdraw from it:
So it'd be nigh-impossible for Atom to catch FS by surprise here. But as leo mentioned: even IF Atom managed to go subatomic and enter Firestorm, he would be vaporized almost instantly... After all, FS is comprised of pure energy akin to the big bang.