A method and apparatus for analysis of a specimen in a microscope are provided. A first survey is performed that collects analytical data from a region of interest on the specimen surface using a first set of conditions. A second survey is performed that collects additional analytical data from selected parts of the region of interest on the specimen surface using a second set of conditions, different from the first set of conditions. The analytical data from the first survey is used to select the parts used for data collection in the second survey and to decide the order in which they are used.