As historical stone masonry structures are vulnerable and prone to damage in earthquakes, investigating their structural integrity is important to reduce injuries and casualties while preserving their historical value. Stone masonry is a composite material that is built with stones and binding mortar. Although experimental campaigns are crucial in understanding the structural behaviour of these walls, the wide spectrum of existing stone masonry typologies and the randomness in geometry and material properties render extensive testing campaigns nearly impossible to account for all the uncertainties and variables. Numerical simulations that explicitly represent the microstructure of the wall (i.e., the geometry and arrangement of the stones) can complement experimental studies. However, methods for generating 3D microstructures were lacking. The focus of this dissertation is to study the geometry of the 3D microstructure of stone masonry walls at multiple scales, which opens unprecedented opportunities for studying the micromechanical behaviour of these walls numerically. The first contribution of this thesis was crafting the first 3D virtual microstructure generator that can cover the main typologies of stone masonry that are frequently found in historical buildings. The herein-created microstructure generator borrowed the conventional packing problem analogy to pack the generated stones inside the boundary of the walls following building and physical placement rules to obtain realistic microstructures. The size spectrum, distribution, interlocking and topology of the generated stones were thoroughly investigated. To quickly and efficiently solve the posed packing problem of each stone, we proposed a general-purpose heuristic algorithm that benefits from Pareto's principle which is commonly known as the $80/20$ rule. This heuristic was called the Pareto sequential sampling (PSS) algorithm as it depends on sampling most of the solutions, using any design of experiment (DoE) method, from a domain that is known to be a prominent pool of solutions. The second contribution was related to studying the topology and roughness of stones and surfaces. The traditional spherical harmonics expansion was used to study the morphology of closed surfaces of the nonconvex stones to estimate their fractal dimension and uniformly remesh the triangulated surfaces to be used in numerical simulations. As the roughness of natural stones changes on a single stone, we similarly studied the morphology of locally sampled rough patches. We developed the spherical cap harmonics and disk harmonics spectral approaches to provide us with information on the roughness and fractal dimension of any isotropic self-affine rough surface. To speed up the numerical integration of these spectral expansions, we proposed new algorithms based on the well-known Kaczmarz orthogonal projection in a non-memory-intensive manner and using reasonable computational times. The developed algorithms were hinged on the conjugate symmetry of the harmonic bases and the sparsity of the real signals to lower the dimensionality of the problem and accelerate the rate of convergence. These spectral methods are considered general-purpose and have multiple applications in various fields such as medical imaging and computer graphics. With this dissertation, we put forward geometrical and topological concepts that make detailed micromechanical simulations of stone masonry walls practical.