We present a thermo-mechanical characterization of organic substrates that accounts for heterogeneity both in the in-plane and out-of-plane directions. Systematic observation of the board files of a number of substrates of commercial interest reveals primarily three recurrent topological arrangements of copper and polymer; for each arrangement, the in-plane effective thermo-elastic properties are calculated via appropriate composite materials models. The averaging process in the out-of-plane direction (i.e. the stacking effect) is performed using standard laminated plate theory. The model is successfully applied to various regions of three organic substrates of interest (mainly differing in core thickness): the analytically calculated effective Young’s moduli (E) and coefficients of thermal expansion (CTE) are shown to be typically within 10% of the experimental measurements. An important attribute of this model is its ability to provide substrate description at various levels of complexity: a few effective properties are outputted that can be useful for further purely analytical investigations; at the same time, the model provides the full stiffness matrix for each region of the substrate, to be used for more detailed finite elements simulations of higher-level structures (e.g. silicon die/underfill/substrate/cooling solution assemblies). Preliminary application of this model to the warp analysis of a flip-chip is presented in the end.