An apparatus for inspecting a sample, is equipped with a charged particle column for producing a focused beam of charged particles to observe or modify the sample, and an optical microscope to observe a region of interest on the sample as is observed by the charged particle beam or vice versa. The apparatus is accommodated with a processing unit adapted and equipped to represent an image as generated with the column and an image as generated with the microscope. The unit is further adapted to perform an alignment procedure mutually correlating a region of interest in one of the images, wherein the alignment procedure involves detecting a change in the optical image as caused by the charged particle beam.