The wide variety of nest architectural designs exhibited by passerine birds allowed them to diversify into a wide variety of ecological niches and terrestrial habitats. At present, very little is known about the mechanics of building these structures. Digitizing natural biological structures such as bird nests provides the opportunity to explore their structural properties and behavior under specific conditions by means of computational manipulations, simulations, and analyses. This study describes a generic algorithm for the digitization and exploration of complex interlocked bird nests, and validates it on nests built by the Dead-Sea Sparrow (Passer moabiticus) in branches of trees using stiff dry branches. This algorithm takes as input computerized tomographic scans of the nest, identifies and isolates each branch entity within the three-dimensional data, and finally extracts the characteristics of each branch. The result is a reliable three-dimensional digital model of the nest that contains a complete geometric dataset per each of its components, e.g. dimensions and contact points with neighboring components, as well as global properties, e.g. density distribution and network structure. Based on these, we were able to simulate various models of the nest construction process. Altogether, the described algorithm and possible derivatives thereof could be a valuable tool in studying the structure-function relationships of similarly complex biological objects, and may provide further insights into the potential selective mechanisms underlying historical evolution of this distinct nest form.