In the present work magnetic brushes under flow conditions and confined inside narrow slits have been studied using Langevin dynamics simulations. It has been observed that the structural properties of these confined magnetic brushes can be tuned via the application of an external magnetic field, and this control can be exerted with a relatively low content of magnetic colloidal particles in the filaments that form the brushes (20% in the present study). The potential of these brushes to perform a separation process of a size-bidispersed mixture of free non-magnetic colloidal particles flowing through the slit has also been explored. Numerical results show that it is possible to induce a two-fold effect on the bidispersed particle flow: a lateral separation of the two types of flowing colloidal particles and an enhancement of the differences in their velocities. These two features are key elements sought in separation processes and could be very relevant in the design of new chromatographic columns and microfluid separation devices.