In this work we prepared Superconductor(SC)/ferromagnet(FM) Nb/Co multi-layers with magnetron-sputtering. The main purpose of this work is to study the effect of different shape of ferromagnetic layers on the superconducting properties of Nb. We expected that after annealing the Co layers can form in-plane ordered magnetic nanoparticles and the effect of ordered magnetic nanoparticles should be very different from randomly oriented nanoparticles and continues magnetic layers. The microstructures have been investigated by means of Low Angle X-ray Diffraction (LAXRD), Atomic Force Microscopy (AFM) and Transmission Electron Microscopy (TEM). Magnetic and transport properties have been studied with Physical Property Measurement System (PPMS) from Quantum Design. The magnetic and transport measurements show that with increase of the thickness of Co layers the superconducting transition temperature (Tc) signifficantly increases for the as-prepared samples. It was reported in the literature that when the thickness of the magnetic layers is in the range of several nanometers, Tc increases and decreases periodically with the increase of the thickness of the magnetic layers. In our samples, however, the thickness of the magnetic layers (several tens nanometers) is much larger than that range and therefore, cannot be explained within the same model. We proposed that the roughness of the interface between Co and Nb layers plays an important role for this behavior. The AFM and LAXRD results show that the maxim roughness of the interface is in the range of 7 until 10 nm, which is comparable to the thickness of Co layers (5 until 20 nm). We introduced one parameter R equal d, where R is the roughness of the interface and d is the thickness of the magnetic layer, to discuss the effect of the interface on the superconducting properties of our sample. When delta more 1, the magnetic layer may be in a non-continues form and only when delta less1 continues magnetic layers can be formed. Based upon nano-scale observations of interfaces topography we can understand that the roughness first increases the area of the interface, which gives stronger proximity effect and, second, enhances the effect of the stray eld on Tc. This effect depends not only the roughness but also the thickness of the magnetic layer. It was found out that the parameter determines the effect of the magnetic layers. The different magnetic properties below Tc for different samples can also be explained by this model. After annealing, Tc of the samples decreased and magnetic properties also became worse than the as-prepared samples. The TEM results show that the Co layers is interconnected and after annealing there is no indication of interdiffusion between Nb and Co layers. More measurements are needed to see if the magnetic layers can induce spontaneous vortices and what the difference is between samples with ordered and randomly oriented magnetic nano-particles.