Three-dimensional printing methods and systems use a derived geometry and aligns anisotropic inclusions in any orientation at any number of discrete volumetric sections. Structural, thermal, or geometry-based analyses are combined with inclusion alignment computations and print preparation methods and provided to 3D printers to produce composite material parts that meet demanding geometric needs as well as enhanced structural and thermal requirements. In one example, optimal inclusion alignment vectors associated with a section of the object are calculated based on specifications for the object, segmenting a three-dimensional model of the object into layer slices, grouping each section within each layer slice having similar alignment vectors and combining the groupings and generating printing instructions for the object according to the grouped alignment vectors.