The atmosphere and ocean structure consists of horizontal regions with characteristic mean flows, waves and turbulence, separated from each other by semipermanent thin layers such as the tropopause or the thermocline. At the same time, within these regions, thin layers are continually appearing and dissipating such as clouds and fronts, which largely determine the weather. There are also sharp variations in the horizontal structure of flow and physical processes separated by thin layers with sloping or vertical boundaries (e.g. ozone hole and the intertropical convergence zone). We review here how the mechanisms of waves, wave-mean flow interactions, turbulence distortion, turbulence-wave transformation and Coriolis forces, determine the formation, location and dynamics of these layers. This review provides perspectives on current methods of calculating these critical regions in large-scale numerical models used for weather and ocean forecasting, and for climate prediction.