A detailed search for emission and absorption lines and an assessment of their upper limits are performed for Suzaku data. The method utilizes a matched-filtering approach to maximize the signal-to-noise ratio for a given energy resolution, which could be applicable to many types of line search. We first applied it to well-known active galactic nuclei spectra that have been reported to have ultra-fast outflows, and find that our results are consistent with previous findings at the similar to 3 sigma level. We proceeded to search for emission and absorption features in two bright magnetars 4U 0142+61 and 1RXS J1708-4009, applying the filtering method to Suzaku data. We found that neither source showed any significant indication of line features, even using long-term Suzaku observations or dividing their spectra into spin phases. The upper limits on the equivalent width of emission/absorption lines are constrained to be a few eV at similar to 1 keV and a few hundreds of eV at similar to 10 keV. This strengthens previous reports that persistently bright magnetars do not show proton cyclotron absorption features in soft X-rays and, even if they exist, they would be broadened or much weaker than below the detection limit of X-ray CCD.