A continuous condition monitoring system to detect and localize railroad track irregularities is achievable with inertial sensors onboard revenue service trains. However, the inaccurate geospatial position estimates of GPS receivers and the non-uniform sampling of inertial sensors adds noise and reduces signal strength. Consequently, the signal-to-noise ratio decreases, which leads to higher rates of false positives and false negatives. Appropriate signal filtering, alignment, and combination from multiple traversals can enhance the signal-to-noise ratio. However, it is not straightforward to determine the best cut-off frequency for the filter. This paper introduces a method that is suitable for any signal filtering approach. The frequency window of the resultant energy and variance of ensemble averaged FFTs informs the best cut-off frequency. The results affirm that a lowpass finite impulse response filter with the selected cutoff frequency progressively increases the signal-to-noise ratio with increasing filter order, thus demonstrating the effectiveness and practicality of the method.