A method, and a corresponding system, are provided for calibrating data of an object measured by different measuring tools, including measuring a Critical-Dimension (CD) and roughness of an object by using a CD-SEM tool, calculating a number of cross section measurement points required for calibration, by statistically processing the roughness of the object, measuring the cross section of the object by using a cross section measuring tool to obtain cross section data at the calculated number of cross section measurement points, calculating the average measurement of the cross section measurement height, and calculating a calibration correction value that is a function of a difference between the average CD measurement of the object and the average measurement of the cross section measurement height of the object.