A system, apparatus and method for magnetically separating a fluid flow passing through a pipeline are provided. A magnetic separator assembly having a plurality of elongate magnetic members is provided. Each magnetic member can have a first end and a second end. A cleaner plate can be provided that can move along the magnetic members. After the magnetic separator assembly is used to collect magnetic particles from a fluid flow in a pipeline, the magnetic separator assembly can be cleaned by sliding the cleaning plate along the magnetic members.