Stone masonry is a multi-age-old construction technique that consists in assembling stones without using binders. In a previous work aiming to understand the dynamic behavior of such structures, a series of reduced-scale experiments had been carried out, including both pseudo-static and true dynamic tests. A coupled plane strain Mixed Discrete-Continuum (MDC) approach had been used to model those experiments. This method showed its limits to retrieve the behavior easily and correctly. In this study, a 3D numerical tool that is based on MDC is employed in comparison to a plane strain approach and has been validated.