The assembly of nanoparticles into complicated, anisotropic shapes has much promise for advanced materials and devices. Developing effective and efficient anisotropic mono-functionalization strategies is an imperative step in realizing this potential. By functionalizing DNA one at a time to the nanoparticle, a DNA-nanoparticle building block could have distinct DNA sequences at different locations on the surface of the particle. Since this technology could incorporate nanoparticles of different composition, generating toolboxes of various nanoparticle building blocks (“nano-toolboxes”) with DNA at defined locations and in defined 3D orientations on a nanoparticle, it promises not only complicated shapes, but also the ability to tune the function of the assembly. The challenges of programmable and scalable multifunctional nanostructure self-assembly with DNA conjugated to nanoparticles are reviewed. The first difficulty is to control the assembly process so that designed products are formed, and unwanted products are minimized. The design problem for nanostructure construction is both physically and computationally complex. Thus, the other major challenge is to devise design methodologies that move nanostructure construction from trial and error to principled approaches. Strategies to overcome these challenges are also presented by realizing greater control over the final shapes and functions of the self-assembled nanostructures. Finally, the future perspectives of nano-toolboxes and their promise in applications such as multifunctional, multicolor, and multimodal contrast nanoagents for medical therapy and diagnostics (theranostics) are described.