A quarantine is a region designated by Fringe Division to be a danger due to incursions from the Prime Universe. Most quarantine regions are encased in amber to prevent anyone from entering or leaving.
Quarantines take place when the fabric of the universe is torn as a result of the universes colliding into another. The Alternate Universe has been patching their world with amber ever since Peter Bishop was stolen from that universe by Walter Bishop at Reiden Lake. The effects of Walter's actions has caused the decay of the alternate universe. Areas in the alternate universe decay as if a black hole takes place inside the earth, sucking all everything into the core.
The air (or space in the area) is scanned by a machine that detects if the fabric of the universe is torn. If the place is deemed unsafe (level 3). The Fringe Division then relocates everyone in the area to a safer place.
The Fringe Division then sends out an Amber Alert.
The area is then covered by a canister of Amber. Gas turns into Amber and stops the area from decaying. This area is then Quarantined. Unfortunately, if someone is trapped in amber, their demise does not mean death, infact they are trapped in suspended animation and dwell on their last thought for however long they are encased in amber.