An imaging system that selectively alternates between a first, non-destructive imaging mode and a second, destructive imaging mode to analyze a specimen so as to determine an atomic structure and composition of the specimen is provided. The field ionization mode can be used to acquire first images of ionized atoms of an imaging gas present in a chamber having the specimen disposed therein, and the field evaporation mode can be used to acquire second images of ionized specimen atoms evaporated from a surface of the specimen with the imaging gas remaining in the chamber. The first and second image data can be analyzed in real time, during the specimen analysis, and results can be used to dynamically adjust operating parameters of the imaging system.