The seismic response of three multi-span masonry structures has been investigated through an advanced macro and micro-modeling FE-based approach. The structures with 1.27, 2.25 and 3.3 vault-to-spring ratios (L/B) are selected. Detailed three-dimensional FE models with a damage plasticity behavior for masonry have been developed, and non-linear dynamic analyses were done. The studies have highlighted the effects of geometrical features on the seismic behavior of the nine structures. The structures were subjected to six near-fault and far-fault accelerations. The structure with a square plan has a lower earthquake coefficient. But, in a rectangular plan with the length of one longer side, the earthquake coefficient increases significantly. It shows that a square plan has more ductility than a rectangular plan. The structure with the square plan showed the best stability. Changing the plan from square to rectangle, the structure's stiffness increases significantly with the increase the number of spans. On the other hand, the one to two-span structures with a rectangular plan have the highest increase in stiffness of about 56 %, which becomes about 23 % with the increase of the third span. The vertical component in near-field accelerations can increase displacement and damage by 83 %. The beginning of the damage process in the structures with the square plan is from the connection of the vault and spring to the roof, but in structures with a rectangular plan, the plastic strain starts from the connection of the spring to the roof. Some far-fault accelerations could have destructive effects, like did near-fault accelerations in the horizontal direction. It is better to state that the remoteness of the accelerations is not the reason for reducing the damage to the structure.