Multi-electrode cuff electrodes is an important component in an implanted functional neural stimulation system. We constructed finite element models to investigate the effects of changing the spatial configuration of electrodes in a cuff electrode system on the noise shielding and activation pattern. The results could facilitate designing of cuff electrodes. For noise resistance, a 2D model with an external noise source was constructed. For activation pattern, two 3D models, a unifascicular and a multifascicular model, were constructed. Three types of electrode configurations, transverse, longitudinal and cross, on both types of 3D models were simulated. Model parameters were changed systematically and simulations were performed. For noise resistance in sensing applications, increasing the cuff length reduced the interference of external noise. For stimulation with three types of electrode arrangement, i.e., transverse, longitudinal and cross, we found cross arrangement was the best one having the advantages of both convex activated region and lower threshold current.