An unconventional approach using the time-of-flight secondary ion mass spectrometry (TOF-SIMS) technique to determine the height topography at the microscale is detailed in this work with an application to cotton paper banknotes. The study was conducted by determining the effect of all related factors and parameters on the height measurement by taking the simplest model made from two Post-it sheets. For each sample, the difference in the TOF of the same secondary ion coming from two different heights was successfully attributed to the step height of the studied areas' topography, which was measured using classic methods. The measurement was independent of the orientation of the topography with regard to the primary ion beam and the electron beam azimuth. Moreover, the adjustment of the extraction gap with different layers has no effect on such measurements. However, a range of the analyzer acceptance energy values could be considered to achieve the expected outcomes only if the different analyzers' component energies are also changing accordingly. Heights between 20 and 180 μm were successfully measured using this new method. An added benefit to this method over other height measurement methods is the ability to discern areas with different chemical compositions, which eventually may help aid understanding of the sample in question.