The accurate prediction of the Upper Troposphere and Lower Stratosphere (UTLS) environment is critical to the success of US Air Force operations. The weapon, reconnaissance, and communication systems may be adversely affected by upper tropospheric ice clouds, high impact optical turbulence (OT) and clear air turbulence (CAT) layers in the UTLS region. Non-homogeneous, anisotropic, shear-stratified flow computations in the UTLS require that a fine mesh be used to encompass all pertinent multiscales. This, coupled with stiff velocity and temperature gradient profiles, presents significant challenges for nesting and adaptive gridding. Our approach is based on vertical nesting and adaptive vertical gridding in nested mesoscale WRF/microscale codes. The inner nest of WRF (1km grid in the horizontal, 150 levels in the vertical) is coupled with a sequence of embedded microscale nests, both horizontally and vertically. The fully three-dimensional, moist, compressible, non-hydrostatic Navier-Stokes equations are solved with a stretched, adaptive grid in the vertical. An adaptive, staggered grid mesh is used in the vertical, with a grid spacing down to a few meters in the UTLS region. For nesting, both lateral and vertical boundary conditions are treated via relaxation zones where the velocity and temperature fields are relaxed to those obtained from the WRF inner nest. Temporal discretization uses an adaptive time-split integration scheme and the Thompson microphysics parameterization scheme. This methodology is applied to the analysis of field data from recent campaigns of measurements. Our real case simulations are based on real initial and boundary conditions from high resolution T799 L91 ECMWF analysis data.