This work comprises the modeling and study of a historical masonry structure which was tested on the shake table of the National Technical University of Athens. An as accurate as possible modeling is required in order to correctly assess the behavioral patterns of the building under seismic load and accurately interpret the results measured during the test. The tested building was constructed at a ½ scale. This is the scale which, with some adjustments, still renders realistic results. The materials used for the construction of the building are stone masonry and, for the floor, wood. Also, the techniques used for the effective construction process were the traditional techniques (i.e.: manual placing of the blocks and the mortar), so the outcome is as realistic as possible. Throughout this work, we will deal with a lot of uncertainties and we will employ a number of finite element models in order to reach the final results which can, afterwards, be accurately interpreted. The present modeling and the experiment which was conducted in the premises of the National Technical University of Athens are part of the NIKER European project. The NIKER (New Integrated Knowledge based approaches to the protection of cultural heritage from Earthquakeinduced Risk) program aims at developing a validating innovative materials.