The capability of assembling nanoparticles into a desired ordered pattern is a key to realize novel devices which are based not only on the unique properties of nanoparticles but also on the arrangements of nanoparticles. While two-dimensional arrays of nanoparticles have been successfully demonstrated by various techniques, a controlled way of building ordered arrays of three-dimensional (3D) nanoparticle structures remains challenging. We report that a variety of 3D nanoparticle structures can be formed in a controlled way based on the ion-induced focusing, electrical scaffold, and antenna effects from charged aerosols. Particle trajectory calculations successfully predict the whole process of 3D assembly. New surface enhanced Raman scattering substrates based on our 3D assembly were constructed as an example showing the viability of the present approach. This report extends the current capability of positioning nanoparticles on surface to another spatial dimension, which can serve as the foundation of future optical, magnetic, and electronic devices taking the advantage of multidimensions.