Spectral peak generation is a recently reported phenomenon that narrow spectral dips of the optical spectrum turn into sharp peaks as they propagate through nonlinear optical fibers. We demonstrated the nonlinear polarization rotation-based spectral peak mode filtering to increase the signal-to-background ratio (SBR). The spectral peaks with almost constant frequency separation were generated from the femtosecond pulses absorbed by the CH4 gas through the highly nonlinear fiber. The generated spectral peaks were filtered through the polarizing beam splitter by the nonlinear polarization rotation, and the SBR was improved from 9 dB to ∼20 dB. The spectral peak generation phenomenon and the mode filtering were numerically confirmed by solving the coupled nonlinear Schrödinger equations. The demonstrated method can generate strong comb modes with wide frequency spacing which are useful for highly sensitive environmental gas sensing spectroscopy. The wavelengths of the spectral peaks are fixed by the absorption spectra of the used gas cells. Therefore, this method can generate high quality spectral peaks of any wavelengths with wide spectral ranges through proper combinations of gas cells.