Recent technological developments in mechanical investigation techniques and nondestructive monitoring of masonry buildings provide today an amount of information, unthinkable up until yesterday. Likewise the techniques of automated laser survey allow a rapid and precise definition of the geometry of a building, with a level of detail never previously reached. On the other hand, the applications to the modeling of complex masonry historical structures are not as widespread, and constitute an interesting subject of research. Despite the fact that numerical modeling techniques based on the finite element method have progressed considerably, and the computing power available is constantly growing. The difficulties that are encountered are manifold, and reside especially on the absence of well consolidated procedures for the definition of the model and for the management of uncertainties. The Asinelli Tower in Bologna is taken as a case study to define a general methodology for the analysis of historical masonry towers. Using the finite element code DIANA (TNO Diana, Netherlands) the difficulties that are typically encountered in building models of increasing complexity are addressed, proposing a general procedure. The study of the tower, although not directed to the formulation of an explicit judgment on the structural stability, has led to the formulation of an anisotropic cracked masonry model, capable of representing the dynamic behavior of the tower with greater efficiency compared to what is available in the scientific literature.