Localisation of axial peaks is essential for height determination in confocal microscopy. Several algorithms have been proposed for reliable height extraction in surface topography measurements. However, most of these algorithms use nonlinear processing, which precludes estimating the peak height uncertainty. A Monte Carlo based standard uncertainty analysis model is developed here to evaluate the precision of height extraction algorithms. The key parameters of this model are the vertical sampling deviation and the size of the scanning pitch. Height extraction uncertainty of the centroid algorithm and nonlinear fitting algorithms were calculated using simulations. Our results offer a reference for selecting algorithms for confocal metrology.