This paper describes the model updating procedure implemented in NOSA-ITACA, a finite-element code for the structural analysis of masonry constructions of historical interest. The procedure, aimed at matching experimental frequencies and mode shapes, allows fine-tuning calculation of the free parameters in the model. The numerical method is briefly described, and some issues related to its robustness are addressed. The procedure is then applied to a simple case study and two historical structures in Tuscany, the Clock Tower in Lucca and the Maddalena bridge in Borgo a Mozzano.