Bluff bodies such as circular and square cylinders are the most important flow models in the aerodynamics, hydrodynamics, and fluid mechanics due to their academic significance and engineering applications such as buildings, towers, bridge piles, offshore structures, heat exchangers, electronic devices, etc. The flow over cylinders in tandem, side-by-side or staggered arrangements represents an importance and complex configuration that is of interest for many engineering applications. For these configurations, the flow interference has an essential role for several changes in the characteristics of the flow. Thus, the dynamic interaction between the structure and the fluid is one of the most fascinating problems in mechanical engineering. In present work, the fluid flow and heat transfer over two side-by-side square cylinders with finite length and wall-mounted (three dimensional geometry) like two side-by-side buildings are investigated at Reynolds number of Re=12000. The aspect ratio (height to side length of square cylinder) and the center-to-center distance between two cylinders are chosen AR=7 and S/d=2-5, respectively. In the flow around a wall-mounted three dimensional cylinder in contrary of infinite cylinder, the combined effects of vortex shedding, tip vortex, base vortex and horseshoe vortex together with downwash and upwash flows are present which it can make the flow structure more complicated. In addition, the interference flow effect of each cylinder on the second one is a reason to provide more complicated flow patterns. In this research, the flow and heat transfer over two geometries are studied. First, flow and heat transfer over two infinite square cylinders in side-by-side arrangement (two-dimensional geometry) are simulated using k-w-SST turbulence model. The results show that there are different flow regimes, including biased or flip-flop regime, synchronized shedding vortex and flow regime with two separate vortex street. Second, flow and heat transfer over two wall-mounted square cylinders in side-by-side arrangement (three-dimensional geometry) are simulated using Large Eddy Simulation (LES). For this case, the instantaneous and mean structure of cylinders wake, global quantities such as force coefficients, Strouhal number and Nusselt number, pressure coefficient, velocity and temperature distribution and also turbulence intensity have been investigated. The aforementioned flow patterns for two dimensional geometry are also observed for three-dimensional geometry just at the middle-height of cylinders. It is found that the drag coefficient, Strouhal number and Nusselt number are lower for three dimensional geometry in comparison with those of two-dimensional geometry. This is due to the effects of free end and wall junction of cylinder flow patterns especially down-wash flow on the cylinders wake structure. It is observed that the flow behavior and related parameters at S/d =2 are quite different in comparison to other distances due to gap flow between two cylinders and their significant interferences effects. Finally, results showed that by increasing distance between two cylinders, flow patterns and related quantities approximately approach to flow over a single cylinder. Keywords: Unsteady flow, Numerical simulations, Large Eddy Simulation, Wall-mounted cylinders, Infinite cylinders, Side-by-side arrangement, Vortex shedding, Heat transfe