Pin-fin arrays are known to enhance heat transfer from heated surfaces and provide important industrial applications such as increasing internal heat transfer to a turbine blade or solar receiver. Several studies on heat transfer characteristics of various pin-fin arrangements and effects of geometrical parameters on heat transfer have been performed in the past. The present paper aims to address main aspects of fluid flow and heat transfer interactions through a pin-fin array with the help of high-fidelity numerical simulations and focuses on three issues. The first one is to evaluate the effect of three dimensional flow physics such as horseshoe vortices and periodic unsteadiness from vortex shedding on the spatial variation of heat transfer. The second target is to analyze the effect of free end clearance in the case of finite height pin-fin arrays with added flow complexity relative to wall-bounded pin-fin arrays, to provide a comprehensive picture of the flow physics introduced by free ends. The third one is to provide a general guideline for the numerical simulation of flows through pin-fin arrays by comparing simulations on reduced span-wise domains with the full multi-row pin configuration, to elucidate the significance of wall effects. In addition, comparison of the flow characteristics in different stream-wise row locations, is performed to establish the domain length where self-similarity might occur with inflow/outflow conditions. All simulations are conducted for low Mach number incompressible flow with temperature as a passive scalar. The current formulation assumes that variations in temperature have no effect on the fluid motion by choosing appropriate thermal boundary conditions that are still within the realistic parameter range for turbine cooling. In this paper, we perform flow simulations using the Large Eddy Simulation methodology. Two numerical codes, one based on a Finite Volume method and the other based on a Spectral Element approach, are benchmarked with each other and validated versus experiments available in the literature (Ostanek and Thole, 2012).