The words male and female are used as classifications (such as in anthropology, or medicine), and they can be used as adjectives as readily as nouns. The words man and woman are more personal descriptors of individuals.
When using these words to describe the subjects of a scientific study, we might find either of these:
•The control group consisted of 26 female and 18 male patients.
•The control group consisted of 26 women and 18 men.
You are right about how your second example sentence sounds "off", but that's because you've mixed the two words:
•The woman pointed the gun at the man. (sounds normal)
•The female pointed the gun at the man. (sounds awkward)
•The woman pointed the gun at the male. (also sounds awkward)
•The female pointed the gun at the male. (sounds acceptable)
However, context could very well override that general guidance. Some of the sentences I've labeled as awkward may sound funny on their own, but they could be just fine in the middle of a lengthy testimony during a courtroom trial, where a long series of questions has set up a scene - i.e., something like this:
"What did you see in the room?"
"There was a woman with a gun, and two people in the doorway."
"Could you tell if those two people were male or female?"
"And what did you notice?"
"There was one male, and one female."
"And what happened next?"
"The woman pointed the gun at the female."
I think that last sentence reads just fine in that context, because the preceding dialog has made it rather easy to follow along.