Confined masonry (CM) is one of the most popular and affordable earthquake-resistant con-struction technology for masonry structures. The reinforced concrete (RC) tie-columns in such construction play a crucial role in improving seismic response. However, their interaction with the masonry warrants a review due to recent changes in masonry construction, which are typical for Southeastern Europe. The modern masonry walls built from clay units are thick to achieve thermal efficiency. The tie-columns size has also increased, but they are narrower than the masonry. A part of masonry thus protrudes from the area confined by tie columns, which can lead to stress concentrations and early onset of damage of the protruding masonry, as was observed in recent tests on such masonry. This paper numerically analyzes this problem using a detailed three-dimensional (3D) finite element (FE) model that can capture this effect. The numerical model was developed in ABAQUS, and uses Concrete Damage Plasticity (CDP) material model to model the brittle response of clay blocks. All input data for the numerical model were obtained by dedicated tests. The results are compared to tests of walls in terms of damage propagation, strength and deformation response and show that damage to the protruding masonry can be successfully modelled. The results show a good alignment with the experiments and can be used for detailed modelling of seismic response of CM masonry structures and further research.