We present an Embedded Boundary with Adaptive Mesh Refinement technique for solving the compressible Navier Stokes equations in arbitrary complex domains; followed by a numerical studies for the effect of circular cylinders on the transient dynamics of the Richtmyer-Meshkov Instability. A PDE multidimensional extrapolation approach is used to reconstruct the solution in the ghost-fluid regions and imposing boundary conditions on the fluid-solid interface, coupled with a multi-dimensional algebraic interpolation for freshly cleared cells. The Navier Stokes equations are numerically solved by the second order multidimensional upwind method. Block-structured AMR, implemented with the Chombo framework, is utilized to reduce the computational cost while keeping high resolution mesh around the Embedded Boundary and regions of high gradient solutions. The versatility of the method is demonstrated via several numerical examples, in both static and moving geometry, ranging from low Mach number nearly incompressible to supersonic flows. Our simulation results are extensively verified against other numerical results and validated against available experimental results where applicable. The effects on the transient dynamics of the Richtmyer-Meshkov instability due to small scale perturbations introduced on the shock-wave or the material interface by a single or set of solid circular cylinders were computationally investigated using the developed technique. First, we discuss the RMI initiated on a flat interface by a rippled shock-wave that is disturbed by a single circular cylinder. Then, we study the effect of introducing a number of circular cylinders on the interface. The arrangement of the cylinders set mimic (in a two dimensional domain) the presence of the solid supporting grid wires used in the formation of the material interface in the experimental setup. We analyzed their effects on the mixing layer growth and the mixedness level, and qualitatively demonstrate the cylinders' perturbation effects on the mixing layer structure. We modeled the cylinders' influence based on their diameters; and showed the model ability to predict the variation of the mixing layer growth for different flow parameters.