We describe new techniques in the construction of optical lattices to realize a coherent atom-based microscope, comprised of two atomic species used as target and probe atoms, each in an independently controlled optical lattice. Precise and dynamic translation of the lattices allows atoms to be brought into spatial overlap to induce atomic interactions. For this purpose, we have fabricated two highly stable, hexagonal optical lattices, with widely separated wavelengths but identical lattice constants using diffractive optics. The relative translational stability of 12 nm permits controlled interactions and even entanglement operations with high fidelity. Translation of the lattices is realized through a monolithic electro-optic modulator array, capable of moving the lattice smoothly over one lattice site in 11 micros, or rapidly on the order of 100 ns.