In order to meet the requirements of shake tables, frequency filtration of seismic input is usually performed before tests. Aiming to study the error of seismic analysis caused by filtering, the artificial seismic waves before and after filtering with four different waveforms were synthesized in this paper. Based on a spring-friction isolation system, the effects of filtering on seismic responses with various spring constants, friction coefficients and envelope functions were investigated. The results show that the maximum acceleration of the pure friction system is not affected by filtering while the error of maximum relative displacement caused by filtering can reach 60% and decreases with the increment of the friction coefficient. For the spring-friction system, the friction coefficient corresponding to a smaller structural seismic response is exactly the most unfavorable friction coefficient for filtering error and hence needs more attention during shaking table tests. Filtering errors based on different waveforms have the same tendency despite some slight differences owing to the different responses.