Safe Zones only appear in Metroid Prime 2: Echoes, on Dark Aether. They are safe areas that shield Samus from the poisonous atmosphere of Dark Aether. She will encounter numerous Light Crystals and Light Beacons that generate Safe Zones, as well as Lightbringers, though since the latter are moving organisms, they have the added benefit of creating moving Safe Zones. She can create these zones by firing at Light Beacons and killing Lightflyers. The Safe Zones also protect Samus from Ing to a certain extent. They can still use their beam attacks, swipe Samus with their limbs if she is close enough and roll through to attempt to possess her, however.
Safe Zones can be enhanced if Samus uses the Light Beam or Annihilator Beam on the Light Crystals/Beacons, and deactivated with the Dark Beam. When hit with the Light Beam, they become energized; if an Ing or a Darkling enters the energized Safe Zone, it will be greatly injured. The only good chance Samus will have to kill them in this method is if she energizes the Safe Zone when the creature is in the area. When hit with the Annihilator Beam, they will be supercharged and will draw in Ing like moths to a flame; once the dark creature enters the Safe Zone, it is destroyed. This is because the light is mixed with darkness, as with the light's destructive tendencies, the Ing are attracted to the dark resonance and are destroyed by light once they are close.
As stated before, Safe Zones can also be momentarily disrupted. If the generator of the Safe Zone is hit by an attack from certain dark creatures or shot with the Dark Beam, the Safe Zone will disappear. This can be fixed by either shooting the generator with the Light Beam, Annihilator Beam, or Power Beam. This will not work when fighting Amorbis, as the darkened generators deflect weapons fire; the only way to restore them is letting them reactivate on their own.