Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the wall force penetration region at different flow conditions. Shear stress results are utilized to calculate the tangential momentum accommodation coefficient (TMAC) between argon gas and FCC walls. The TMAC value is shown to he independent of the now properties and Knudsen number in all simulations. Velocity profiles show distinct deviations from the kinetic theory based solutions inside the wall force penetration depth, while they match the linearized Boltzmann equation solution outside these zones. Afterwards, surface effects are studied as a function of the surface-gas potential strength ratio (ϵ wf/ϵff) for the shear driven argon gas flows in the early transition and tree molecular flow regimes. Results show that increased ϵwf/ϵ ff results in increased gas density, leading towards monolayer adsorption on surfaces. The near wall velocity profile shows reduced gas slip, and eventually velocity stick with increased ϵwf/ϵ ff. Similarly, using MD predicted shear stress values and kinetic theory, TMAC are calculated as a function of ϵwf/ϵ ff and TMAC values are shown to be independent of the Knudsen number. Results indicate emergence of the wall force field penetration depth as an additional length scale for gas flows in nano-channels, breaking the dynamic similarity between rarefied and nano-scale gas flows solely based on the Knudsen and Mach numbers