Numerical simulations using the Coupled Ocean and Atmosphere Prediction System (COAMPS) are made for several selected cases during the JES period when adequate measurements were available. The objective of this study is to understand the model behavior by direct inter-comparisons with observations for several cases and understand the model sensitivity to various parameters in the surface flux and boundary layer parameterization. One of the major findings of our study is the close interaction between the two components of the mesoscale model: the surface flux parameterization and the boundary layer parameterization. The surface sensible and latent heat fluxes are very sensitive to variables in boundary layer parameterization such as the formulation for boundary layer length scale. This strong sensitivity can be traced to modifications to boundary layer mean properties that are directly used in the surface flux calculations. Results on these sensitivity tests will be shown together with direct comparisons between the measured and simulated boundary layer height, mean vertical structure, and its variation along the flight track under different large-scale and boundary layer conditions.