Hi @soutomiguel,
In 2D, Empirical Bayesian Kriging will filter some measurement uncertainties by assuming the nugget effect is entirely measurement error, but it assumes that the measurement error is the same for every feature.
If you want to using different measurement errors for different features in EBK in 2D, it is simpler to do with the EBK Regression Prediction tool. The tool requires at least one raster as an explanatory variable, but if you give a constant value, it is equivalent to not using an explanatory variable. Use the Create Constant Raster tool, and set the constant value to the mean of the elevation values.
Hope that helps! -Eric