This paper details the generation of multi-scale flow structure in a package with heat sources. The model is based on abandoning two common assumptions (1) the assumption that there are many channels (components) in the package, which is traditionally made to exploit simplifications due to symmetry, and (2) the assumption that the heat-generating components have negligible thickness. Numerical simulations document the flow stagnation and separation generated by blunt heat sources, and the effect of these flow phenomena on the optimized internal flow structure. The effect of asymmetric thermal boundary conditions on the optimal spacing between heat-generating plates is significant. If the package has some channels with symmetric boundary conditions, and some with asymmetric boundary conditions, then the optimal structure has multiple spacings. The effect of freedom on design performance is documented by optimizing competing configurations that have different numbers of degrees of freedom. (c) 2005 Elsevier Ltd. All rights reserved.