When I was a Christian I had no problem with the concept of the soul, despite the fact that I'd never really figured out exactly what a soul was. Now, as an atheist, I recognize my consciousness as the result of emergent properties of the network of neurons in my brain, rather than a manifestation of a vague supernatural entity.
This presents some interesting possibilities. For example: Let's suspend disbelief for a minute and imagine that, after our death, our brains could be reconstructed into an exact replica of its form at any point in our lives - completely intact with its electrical activity and such - and placed into a matching body.
Is the consciousness of this brain ours?
As a Christian I would have definitely answered this with "of course not," since what made me "me" wasn't just my brain, but my soul. I suppose, in essence, that's what I defined the soul to be - a metaphysical aspect of my existence that made me "me". It was something that wasn't permanently attached to the body.
As an atheist I'm not entirely sure. It depends on how I define "me". Is continuity of consciousness a requirement? If so, my answer would again be "of course not", because my consciousness would be undeniably discontinuous. Let's not pick nits about whether or not sleep counts as a discontinuity; technically, I could be partially conscious while I sleep, inasmuch as my brain continues to function.
But if what defines "me" is really nothing more than the state of a neural network, I suppose the reconstructed brain technically could be me. (Interestingly enough, as I was typing that sentence I had to struggle to keep from ending it with "but not really me". That's the old dualistic impulse showing through - the idea that we're composed of both physical brain and non-physical mind.)
The problem with this scenario (apart from its implausibility) is that, given this sort of technology, we could just as easily reconstruct the brain while we're still alive. A dualist body-soul worldview would maintain that there's only one "me" here - that the rest would be missing a soul, a vital essence, a spirit, etc., and thus wouldn't be "me". But a purely naturalistic, material worldview would be utterly incapable of distinguishing between the various copies. They would each be utterly convinced that their experience had been continuous, apart from the moment where they were first "booted up" (since they would remember being in one place in one instant and in another in the next). The only difference between the various copies would be the physical continuity.
Which brings me to an interesting conclusion, which you may or may not agree with: Regardless of whether we believe or don't believe in a dualistic worldview, what we define as "me" would not be threatened by the production of identical copies of our bodies and minds. A dualist would likely see "me" to be "that which has the soul", while a materialist would see "me" as "the one with continuity of physical presence and consciousness".
That's enough for now... this "me" is ready for bed.