This paper presents a methodology for automated, portable thermography, for the acquisition of high-resolution thermal image mosaics supporting the non-destructive evaluation of historic structures. The presented approach increases the spatial resolution of thermal surveys to a level of detail needed for building scale analysis. The integration of a robotic camera platform enables automated alignment of multiple images into a high-resolution thermal image mosaic giving a holistic view of the structure while maintaining a level of detail equaling or exceeding that of traditional spot surveys using existing cameras. Providing a digital workflow for automated data and metadata recording increases the consistency and accuracy of surveys regardless of the location or operator. An imaging workflow and instrumentation are shown for a case-study on buildings in Florence, Italy demonstrating the effectiveness of this methodology for structural diagnostics.