A charged-particle microscope with Raman spectroscopy capability and a method for examining a sample using a combined charged-particle microscope and Raman spectroscope. The method includes imaging a region of a sample by irradiating the sample with a beam of charged particles from the microscope; identifying a feature of interest in the region using the microscope; radiatively stimulating and spectroscopically analyzing a portion of the region comprising the feature of interest using a light spot of a width D from the spectroscope, wherein the feature of interest has at least one lateral dimension smaller than width D and, prior to using the light spot of the width D from the spectroscope, an in situ surface modification technique is used to cause positive discrimination of an expected Raman signal from the feature of interest relative to an expected Raman signal from the part of the portion other than the feature of interest.