Soul Traps were machines designed by Memnarch. He used them to populate Mirrodin, by abducting inhabitants from other planes.
The abductions went on for centuries. When Glissa eventually killed Memnarch, all the existing soul traps were destroyed. Upon Memnarch's death, Karn could finally return to his plane. He could restore the souls of everyone that died, using the power of Glissa's spark to cast the spell. The kidnapped inhabitants were returned to their long forgotten homes. This was known as "The Vanishing" by their descendants, who remained on the plane.
The end of the Fifth Dawn novel implies that the escapees were returned to their old lives on their home plane fairly intact (without their metallic bodyparts). It is implied that they picked up where they left off, perhaps without even remembering the events that befell them on Mirrodin.
Remnants of the soul traps are studied by the Phyrexians of the Progress Engine, who hope to reverse their effect to spread phyresis across other planes.