I have an atheist friend from my distant past who is amazed, and at times amused, that I believe in spiritual realities, especially:
1) A non-physical, immaterial being - AKA God;
2) spiritual, unembodied beings - AKA angels and demons;
and 3) the human soul - AKA you.
But of course. A real atheist would think this about someone like me. Because, on the atheist worldview (philosophical naturalism), immaterial things cannot exist. An atheist who believed in spiritual beings (and objective moral values) is a poor village atheist who has not understood the logic of their foundational belief-claim.
Such is the nature of worldviews; viz., one sees other worldview-beliefs as amusing and absurd. I'm no exception here, since I find the intra-worldview beliefs of atheism absurd, if not at times amusing. I tilt my head in wonder at my atheist friend's intra-atheistic discussions, since I find philosophical naturalism replete with intractable problems. I could never rationally accept such beliefs. (Like, e.g., downright funny [to me] atheistic claims to be "brights" and "freethinkers" when, on philosophical materialism, neither the "mind" nor "free will" exists [e.g., see Daniel Dennett et. al.].)
The atheist who bwa-ha-ha's at my belief in nonphysical realities is like the chess player who laughs at the football player because they believe in field goals. Put in a Wittgensteinian way, the language games of atheism and theism lack significant overlap in terms of their core beliefs. If one wants to have meaningful discussion one must formulate and evaluate on the level of "worldview," and not on intra-worldview matters.
As for me - I believe in God, I believe persons have souls, and I believe in spiritual beings such as angels and demons.
For some philosophical assaults on philosophical naturalism that I am familiar with see, e.g.:
The Waning of Materialism, Robert Koons and George Bealer, eds.
"Twenty-three philosophers examine the doctrine of materialism find it wanting. The case against materialism comprises arguments from conscious experience, from the unity and identity of the person, from intentionality, mental causation, and knowledge. The contributors include leaders in the fields of philosophy of mind, metaphysics, ontology, and epistemology, who respond ably to the most recent versions and defenses of materialism. The modal arguments of Kripke and Chalmers, Jackson's knowledge argument, Kim's exclusion problem, and Burge's anti-individualism all play a part in the building of a powerful cumulative case against the materialist research program. Several papers address the implications of contemporary brain and cognitive research (the psychophysics of color perception, blindsight, and the effects of commissurotomies), adding a posteriori arguments to the classical a priori critique of reductionism. All of the current versions of materialism-reductive and non-reductive, functionalist, eliminativist, and new wave materialism-come under sustained and trenchant attack. In addition, a wide variety of alternatives to the materialist conception of the person receive new and illuminating attention, including anti-materialist versions of naturalism, property dualism, Aristotelian and Thomistic hylomorphism, and non-Cartesian accounts of substance dualism." (from amazon.com summary)
See also Naturalism, by Stuart Goetz and Charles Taliaferro.
And J. P. Moreland, The Recalcitrant Image: Human Persons and the Failure of Naturalism.
My recent book is Praying: Reflections on 40 Years of Solitary Conversations with God.