I am secular humanist, as far as my flavor of atheism. Scientifically, most humans have what is known as empathy, or the ability to imagine what another human would feel in another's shoes. It is one of the reasons sad movies make most of us sad, we empathize with the character that is hurt.
So in order to decide what is moral for an individual one must simply ask themselves how they feel about having the same thing done to them.
I don't want to be robbed, therefore I don't rob other people.
I don't wan to be lied to, so I try not to lie to others.
I don't want to be raped to death, so I don't rape little girls to death.
I can also empathize with the loss I would cause others if I was to kill their friend or family member and I would rather not live with that.
As far as Scientific method:
Question: Is it wrong according to society to rape little girls to death?
Hypothesis: I believe it is wrong and I assume society agrees with me.
Data: Almost all countries punish rape with prison or castration. Murder is considered wrong by all countries throughout the world.
Conclusion: Rape and murder is considered wrong by most of our entire species around the world. Therefore for humans at least, it is morally wrong. Simplistic verson but it works.