Nanoparticles with concentric layered structures were generated from a lamellae-forming poly(styrene-b-isoprene) diblock copolymer using controlled precipitation from a tetrahydrofuran/water mixture. Chloroform, a good solvent for both blocks, was used to swell and anneal the nanoparticles suspended in aqueous media. The three-dimensional morphologies of particles were reconstructed by transmission electron microtomography throughout the process of solvent annealing. A transition from concentric lamellae to PI cylinders in a PS matrix occurred upon annealing, presumably due to a slight selectivity of chloroform for PS. These cylindrical microdomains were further divided into PS-core PI-shell spherical structures in a PS matrix upon extended annealing, a structure that is unique among reported microphase separated morphologies of diblock copolymers.