In this paper, we discussed a method for the measurement and characterization of a three-step height sample using a stylus profiler. The original measurement data were processed by a polynomial fitting based algorithm to reduce low frequency artefacts. A low pass filter with the cutoff frequency of 0.8/mu m was used to remove the high frequency noise, and a ten order polynomial was used to effectively remove the low frequency artefacts. The experimental results indicated that the uncertainties of the step heights were between 1 nm and 2.2 nm. Furthermore, the deposition rate of the step films with uncertainty was calculated as an application of the sample measurement. The results indicate that the deposition rate for the step films based on the measurement of the stylus profiler was consistent with that of a spectroscopic ellipsometer. (C) 2016 Published by Elsevier B.V.