*The structures of matter does not comes from the structures of elementary particles* 

From the standard model of particle physics, all massive particles get their masses from the Higgs field couplings and these masses are just energies bounded-intrinsically to the particles. Therefore all the masses we see around as is just the sum of intrinsically-bounded and potential energies. 
 
This intrisic-bounded energy or rest mass together with other quantum numbers like spin, elctric charge is what gives a particle a unique identity and structure. Even the atoms do not have structure because of the structures of its constituents particles. For example, we know that a atom is 99.99% empty, for comparison, if we assume a neucleus to be coin sized sphere then a atom would be big-football-ground sized sphere!. The 3d structure of an atom is not because of structures of nucleus or/and electron but because of the electromagnetic field due to p and e- filled within the full atom.

If the string theory is true, all the particles present in the universe are nothing but originate from the same fundamental phenomenon of vibrating strings. Different modes of vibration of different strings gives different particles(one string mode ~ one particle). These particles structures, again, does't depend directly on 1d-strings, it depends on energy or field between string and particle radius. For comparison, if we assume a string to be of the size of a tree then the minimum size of an elementary particle is around the size of the whole solar system! i.e., an elementary particle is much more emtier then an atom.