Do they have a weak point? Generally headshots do more damage to enemies, and an Atlas is a pretty fearsome foe. I know using biotic/tech powers can speed up the destruction by chewing through shields and then armor, but is there a particular point on it that I can be aiming for?
In the "Enemy Tips" section of the manual (which I found with the help of this post, there's the following advice on fighting Atlus':
The Atlas is a hulking death machine with powerful armor, shields, and weapons. Shatter the canopy to expose the pilot.
Atlases have multiple weak points.
In Single Player, targetting the cockpit is very effective if you're using weapons that have a reasonable chance to shatter it and allow you to hijack the vehicle (Sniper rifles in particular).
If this isn't an option, you'll want to target the plates at the Knees, Shoulders, and Groin, which when destroyed, will cause the Atlas to take a large spike of damage, or target the thrusters mounted on the Atlas's back, which are a notably soft target, and, better yet, if you're able to shoot at those, the Atlas isn't shooting at you.