With molecular-scale materials, devices and fabrication techniques recently begin developed, high-density computing systems in nanometer domain emerge. An array-based nanoarchitecture has been recently proposed based on nanowires such as carbon nanotubes (CNTs) and silicon nanowires (SiNWs). High-density nanoarray-based systems consisting of nanometer-scale elements are likely to have many imperfections; thus, defect-tolerance is considered as one of the most significant challenges. In this paper we propose a probabilistic yield model for the arraybased nanoarchitecture. The proposed yield model can be used 1) to accurately estimate the raw and net array densities, and 2) to design and optimize more defect andfault-tolerant systems based on the array-based nanoarchitecture. As a case study, the proposed yield model is applied to the defect-tolerant addressing scheme called h-hot addressing and simulation results are discussed.