In this study we present a set of guidelines for the design of current carrying micro-conductors/micro-coils (MCs) for magnetic nanoparticles manipulation in biomedical applications. Precise spatial manipulation requires steep magnetic field gradients and due to the consequences of scaling laws, these gradients should be maximized as the size of the particle reduces. Conventional planar coils have many construction and functional limitations, such as generating only small magnetic field gradients, Joule heating, and limited ability to move particles with high spatial resolution. On the other hand, micro-coils can provide a satisfactory solution to all these problems. The geometrical and structural parameters play significant roles in determining the ability to move guide and transport nanoparticles. Design guidelines were generated from a detailed theoretical treatment and finite element analysis (FEA). The spatial distributions of magnetic fields, field gradients and magnetic forces on particles were simulated using FEA for different geometrical/structural parameters and wire arrangements. An array of wires create a chain of magnetic potential wells that are controllable in terms of magnitude and direction and therefore can be used to control the motion and position of magnetic nano-particles by tuning the current through the array.