A process for 3D programmed self-assembly of lithographically printable microscale polymer particles using ssDNA hybridization as the associative force is described. We report our progress in establishing the unit processes required for 3D programmed self-assembly and demonstrate the successful fabrication and sequence-specific self-assembly of covalent ssDNA-functionalized parallelepipeds with dimensions in the sub 10 μm regime characterized by optical microscopy and imaging flow cytometry. This technology has the potential to produce parallelepiped particles with different ssDNA on each facet.