An improved microscope stage mount with built-in fiduciary markers is used for fluorescence microscopy, and comprises: (a) an optically-transparent glass plate adapted for specimen mounting and microscope viewing and comprising a specimen mounting area; and (b) a defined and ordered, two-dimensional microscopic array of fiduciary markers, wherein the markers are polymeric pillars affixed to the plate about the specimen mounting area, wherein the markers provide a three-dimensional spatial reference for the specimen.