We present the first analysis of frame-indifferent (objective) fluxes and material vortices in Large Eddy Simulations of atmospheric boundary layer turbulence. We extract rotating fluid features that maintain structural coherence over time for near-neutral, transitional, and convective boundary layers. In contrast to traditional analysis of coherent structures in turbulent boundary layers, we provide the first identification of vortex boundaries that are mathematically defined to behave as tracer transport barriers. Furthermore, these vortices are indifferent to the choice of observer reference frame and can be identified without user-dependent velocity field decompositions. We find a strong agreement between the geometric qualities of the coherent structures we extract using our new method and classical descriptions of horizontal rolls and convective cells arising from decades of observational studies. We also quantify trends in individual vortex contributions to turbulent and advective fluxes of heat under varying atmospheric stability. Using recently developed tools from the theory of transport barrier fields, we compare diffusive momentum and heat barrier fields with the presence of rolls and cells, and determine a strong connection between heat and momentum orthogonality with the physical drivers of roll-cell transformation. This newly employed frame-indifferent characterization of coherent turbulent structures can be directly applied to numerical model output, and thus provides a new Lagrangian approach to understand complex scale-dependent processes and their associated dynamics. As uniform temperature wind flows over flat terrain that is the same temperature as the air, special eddies, called horizontal rolls, begin to appear in the wind and organize the flow into quasi-recurrent patterns. When air flows over terrain that is much hotter than the air, the air warms and begins to rise and subsequently cool. This gives rise to a different kind of organizing structure, the convective cell, much like you see in fluids on a warm stove. The physics of the transition from roll structures to cell structures in the atmosphere is poorly understood, but important for quantifying exchanges of energy and moisture between the land, ocean, and atmosphere. In the present research, we utilize recent advances from nonlinear dynamical systems to explicitly identify the boundaries of individual coherent fluid structures, and quantify their role in the transport of momentum and heat. This gives us a new way to objectively quantify atmospheric fluxes and determine how much a certain eddy is behaving like a roll or a cell. Lagrangian-Averaged Vorticity Deviation (LAVD) identifies eddy boundaries in large eddy simulations of near-neutral and convective atmospheres LAVD contour eddies exhibit specific frame-indifferent momentum and heat transport characteristics for different atmospheric stabilities Differentiating roll and convective cell type coherent structures is possible via the orthogonality of momentum and heat barrier fields