Wavelength scanning interferometry (WSI) is a technique for measuring surface topography that is capable of resolving step discontinuities and does not require any mechanical movement of the apparatus or measurand, allowing measurement times to be reduced substantially in comparison to related techniques. The axial (height) resolution and measurement range in WSI depends in part on the algorithm used to evaluate the spectral interferograms. Previously reported Fourier transform based methods have a number of limitations which is in part due to the short data lengths obtained. This paper compares the performance auto-regressive model based techniques for frequency estimation in WSI. Specifically, the Burg method is compared with established Fourier transform based approaches using both simulation and experimental data taken from a WSI measurement of a step-height sample.