The Guide to the Expression of Uncertainty in Measurement has some limitations, especially for systems with complex mathematical models. In this article, two alternative methods to obtain the measurement uncertainty (Monte-Carlo simulation and calibration based on experimental measurement) are compared. These methods are widely used to calculate the measurement uncertainty of measurement systems. The advantages and disadvantages of these two methods are going to be studied estimating the uncertainty of the flatness measurement using a system based on laser triangulation. The measurement system captures images of the laser plane projected in the surface to be digitalized. The laser points in each image are identified and extracted and transformed into 3D coordinates to calculate the flatness of the surface. The influence of different factors will be characterized and the results of the estimation of the uncertainty with both Monte Carlo simulation and the calibration based on experimental measurement will be compared as well as the characteristics and requirements of each procedure.