Unless the fabrication error control is well treated, it easily causes overetched fabrication errors, which causes the resonant peak value deviation during the fabrication process of guided-mode resonant filters (GMRFs). Hence, the fabrication error control becomes a key point for improving the performance of GMRF. We find that, within the range of the groove depth from 93 to 105 nm, the relationship between the overetched error and the resonant peak value deviation is nearly linear, which means that we can compensate the reflectance response deviation and reduce the resonant peak value deviation by the method of covering the layer film on the GMRF. Simulation results show that the deviation is compensated perfectly by this way.