An atheist who does not believe in any supernatural forces that can never be explained by natural laws is not going to be able to incorporate beliefs in souls or other supernatural escape routes to immortality.
We are learning how mental properties including emotions, sensory awareness, cognition, memory, can all be correlated with actions performed in different regions of the brain. We have a sense of mind that is independent of the body, and controls the actions of our body -- but this is revealed to be an illusion every time new experiments are done to study volition and intentionality with subjects wired up to some kind of brain imaging device.
Ever since the first experiments by Benjamin Libet over 20 years ago, the pattern has been consistent -- identifiable brain activity precedes the mental awareness of making the decision. It's more correct to consider a conscious decision as the brain bringing a decision to our conscious awareness, than an independent mind making a free will choice to decide.
Other studies from neuroscience on patients with brain injuries, disordered thinking, and especially the split-brain patients, tells us over and over again, that we do not understand the nature of our own minds. Our sense of conscious, unified mind likely comes from nothing more than the need to create a sense of concern for our physical bodies, and a way to distinguish between our physical bodies and the world around us.
What all this means to me is that our minds are a product of the brain interacting with our bodies, and a belief in a mind that is separate from the body, and will live on after death is a byproduct of our fear of death, which drives our need for self-preservation. So an atheist who is a naturalist, has no choice other than accept the fact that without a physical body, there is no mind to go on to an immortal afterlife.