Magnetic separators that clean the fluid stream from impurities, protect the installations in numerous industries. This paper introduces a graphical user interface (GUI) which proposes an optimized coil separating magnetic particles with a radius from 1 up to 500 μm. High gradient magnetic fields are employed in an arbitrary user defined fluidic channel which is made of a nonmetallic material. The effects of coil parameters are studied and adjusted to design an optimum coil with a minimum Ohmic loss. In addition, to design the coil scheme based on the particle movements, a mathematical particle-tracing model within the fluid channels has been utilized. In comparison to conventional magnetic separators, this model is reconfigurable by the user, produces a weaker magnetic field, allows for continuous purifying and is easy to install, with high separation efficiency. The presented GUI is simple to use, where the coil’s manufacturing limitations can be specified.