Method for measuring a sample and microscope implementing the method

A method for measuring a sample with a microscope that has a focusing plane, the method comprising the steps of:

• positioning the sample relative to the microscope such that the focusing plane has a first angle with respect to a top surface of the sample,
• scanning the sample using the microscope with the focusing plane having the first angle with respect to the top surface of the sample,
• computing a confidence distance based on the first angle, and
• selecting at least one among a plurality of alignment markers on the sample for performing a lateral alignment of the scanning step and/or for performing a lateral alignment of an output of the scanning step,
• wherein the at least one alignment marker selected at the selecting step is chosen among the alignment markers placed within the confidence distance from an intersection of the focusing plane with the top surface.