High gradient magnetic separation (HGMS) has long been used as an efficient solid/liquid separation technique in the mining and metallurgical industries. Its potential applications in food, biological and pharmaceutical areas have recently attracted increasing attention. The design HGMS process suitable for emerging applications in these areas has become an important topic around the world. In this work, the trajectories of magnetic particles are simulated in separation column with combined magnetic and flow fields. The fields and forces are calculated with finite element method (FEM). Based on the particle trajectories, the capture performance of single round wire, single non-round wire and multi-wire array are evaluated. In order for our model to be scalable, all governing equations are non-dimensionalized and three dimensionless numbers (Reynolds number, dimensionless characteristic magnetic force and magnetic force based Grashof number) are used for the analysis of particle trajectories. The influences of three dimensionless numbers and other parameters on the capture efficiency are investigated. The dynamic process of particle buildup growth and its effect on flow field and magnetic field are also addressed in this work. With clear physical and mathematical descriptions, a continuous separation concept of simultaneously collecting and removing magnetic particles is proposed and evaluated. All methods and conclusions presented here can be extended to novel magnetic separator design and help us understand the entire separation process.