Three-dimensional carbon nanotube (CNT) forest microstructures are synthesized using sequenced, site-specific synthesis techniques. Thin-film layers of Al2O3 and Al2O3/Fe are patterned to support film-catalyst and floating-catalyst chemical vapor deposition (CVD) in specific areas. Al2O3 regions support only floating-catalyst CVD, whereas regions of layered Al2O3/Fe support both film- and floating-catalyst CNT growth. Sequenced application of the two CVD methods produced heterogeneous 3D CNT forest microstructures, including regions of only film-catalyst CNTs, only floating-catalyst CNTs, and vertically stacked layers of each. The compressive mechanical behavior of the heterogeneous CNT forests was evaluated, with the stacked layers exhibiting two distinct buckling plateaus. Finite element simulation of the stacked layers demonstrated that the relatively soft film-catalyst CNT forests were nearly fully buckled prior to large-scale deformation of the bottom floating-catalyst CNT forests.