A separation system for flow enhanced non-linear magnetophoretic separation of magnetic particles of a first and second type provided within a sample, comprising: a magnetophoresis chip assembly device comprising: a flow chamber having an inlet for introduction of the sample as a flowing sample and an outlet, the flow chamber having a flow path in a first direction between the inlet and outlet, the flow path comprising first and second fluid paths located side by side and having fluid communication therebetween to allow for magnetic particles of the first and second type to be transported from the first fluid path to the second fluid path, wherein a micro magnet array is provided proximal to the first fluid path; and the second fluid path defines a flow separation channel; a flow controller configured to apply flow to the flow chamber such that particles within the sample travelling in the first and second fluid paths experience hydrodynamic forces affecting their movement in the direction of the flow path, wherein the flow controller provides control of the rate of flow of a sample in each of the first and second fluid paths and configured to apply flow continuously; a magnetic module comprising electromagnets (170a, 170b, 170c) and a controller (171, 172), the magnetic module configured to apply an external rotating magnetic field to the first fluid path of the magnetophoresis chip assembly device such that particles within the sample travelling in the first fluid path operably experience an induced magnetic field based on the interaction of the rotating magnetic field and the magnetic field of the first micro magnet array proximal the first fluid path; the magnetic module further configured to apply the rotating magnetic field in a second direction substantially perpendicular to the direction of flow, and the rotating magnetic field is selected to effect transport of particles of the second particle type from the first fluid path to the second fluid path; wherein, taking account of the properties of the particles of the first type and second type, and the critical and threshold frequencies at which the particles of the first and second type are responsive to the rotating magnetic field, the separation system is configured to: control the frequency of the rotating magnetic field, and control the rate of flow of the sample in the first fluid path wherein the frequency of the rotating magnetic field and the rate of flow of the sample are tuned relative to each other to effect a retention of particles of the first type in the first fluid path and transport of particles of the second type to the second fluid path and to provide separation of the particles of the first type from particles of the second type in the first fluid path. a flow chamber having an inlet for introduction of the sample as a flowing sample and an outlet, the flow chamber having a flow path in a first direction between the inlet and outlet, the flow path comprising first and second fluid paths located side by side and having fluid communication therebetween to allow for magnetic particles of the first and second type to be transported from the first fluid path to the second fluid path, wherein a micro magnet array is provided proximal to the first fluid path; and the second fluid path defines a flow separation channel; a flow controller configured to apply flow to the flow chamber such that particles within the sample travelling in the first and second fluid paths experience hydrodynamic forces affecting their movement in the direction of the flow path, wherein the flow controller provides control of the rate of flow of a sample in each of the first and second fluid paths and configured to apply flow continuously; a magnetic module comprising electromagnets (170a, 170b, 170c) and a controller (171, 172), the magnetic module configured to apply an external rotating magnetic field to the first fluid path of the magnetophoresis chip assembly device such that particles within the sample travelling in the first fluid path operably experience an induced magnetic field based on the interaction of the rotating magnetic field and the magnetic field of the first micro magnet array proximal the first fluid path; the magnetic module further configured to apply the rotating magnetic field in a second direction substantially perpendicular to the direction of flow, and the rotating magnetic field is selected to effect transport of particles of the second particle type from the first fluid path to the second fluid path; wherein, taking account of the properties of the particles of the first type and second type, and the critical and threshold frequencies at which the particles of the first and second type are responsive to the rotating magnetic field, the separation system is configured to: control the frequency of the rotating magnetic field, and control the rate of flow of the sample in the first fluid path wherein the frequency of the rotating magnetic field and the rate of flow of the sample are tuned relative to each other to effect a retention of particles of the first type in the first fluid path and transport of particles of the second type to the second fluid path and to provide separation of the particles of the first type from particles of the second type in the first fluid path. control the frequency of the rotating magnetic field, and control the rate of flow of the sample in the first fluid path