Abstract: In 2D and 3D, the magnetic flux density from a micro electromagnet used for magnetic bio-separation was simulated with FEMLAB software. Due to the complexity of the structure, a fine meshing of the 3D structure is not possible. In order to minimize the memory consumption by reducing the size of the space domain surrounding the magnetic structure and by using a relatively coarse mesh, the effects of reducing the size of the space domain and using a coarse mesh that it is possible to perform a reference simulation with a large space domain and a fine mesh, and the errors made by the approximations were quantified. 3D simulations were carried out with space domain and coarse meshing conditions identical to those in 2D simulations, and it is shown that the approximations in 3D simulations result in an underestimation of the order of 10%. The magnetic structure of 3D simulations can be compared with that of 2D simulations.