ATOMINE

Secret zones are usually hidden inside of pillars. Whenever you see pillars (the very thin ones that don't share the same design as the regular level walls) shoot at them and you will sometimes uncover secrets such as a portal to a secret room or a blue module orb.

Oftentimes, you may destroy a pillar while fighting off enemies and not even realize it. A secret zone portal is like the green or red portal you see at the end of levels, but this one is much harder to see, almost transparent. Stand on the portal and it will take you to a small secret zone with an item. This will unlock the achievement.