We have presented a controllable and human-readable polynomial neural network (CR-PNN) that is the first human-readable neural network. One can imagine its influence on system identification. Subsequently, we developed a relation spectrum in a medical application, which is likely to stand alongside the Fourier spectrum. However, the system analysis methodology is incomplete in contrast to signal processing methodology. Here, we presented the system filters for the first time. In this paper, we used the simulation system to verify the availability of the system analysis methodology. The system analysis methodology showed great properties in system identification and filter. The contribution of this paper is the system analysis methodology: transform method (CR-PNN), relation spectrum, and system filter design.