We investigate the directed self-assembly (DSA) of cylinder-forming block copolymers inside extended guiding templates of different sizes and shapes. We focus in particular on templates that promote the formation of linear arrays of two or three cylinders for contact hole multiplication. Using self-consistent field theory (SCFT) simulations, we uncover the existence windows for two- and three-cylinder arrays and assess their stability relative to other defective morphologies present in the templates. From SCFT simulations, templates in which three DSA cylinders are the lowest free energy configuration are more prone to defective morphologies in comparison to narrower templates with a two cylinder ground state. The size, placement and pitch of the defect-free structures are estimated for different template sizes and shapes. Beyond the thermodynamic description of the self-assembly process and the ensuing equilibrium properties, we also consider the equally important issue of the kinetics of melting of defects into perfect structures. Using the string method, we compute the most probable kinetic pathways that anneal elementary defects into a desired perfect array of cylinders. Similar to our findings on defectivity levels, defects in three-cylinder-friendly templates are associated with high kinetic barriers > 8 kT while their counterparts in narrower templates more readily dissipate into two-cylinder states after crossing barriers < 2 kT. (c) 2014 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys. 2015, 53, 317-326