How can 0-dimensional particles or 1-dimensional strings be 3D matter? According to the latest information we got

String theory is a theoretical framework in which the point-like
  particles of particle physics are replaced by one-dimensional objects
  called strings.

We know that anything we've ever seen on a microscopic level or a gigantic level that matter has thickness? let it's thickness be 1.6 x 10-35 m (Plank length) or let it be 1 m , It has some thickness. Right? So everything we've seen is 3-dimensional right? no matter how much we zoom , we get protons that have thickness.So if matter has thickness then how can we say that Something is "1-dimensional". 

Anything that's 3D is made up of something 3D. If we add 0 thickness we get 0 thickness but if we add some thickness like atoms and molecules we get 3D matter as the constituents have thickness.

Then how particles of particle physics are replaced by one-dimensional objects called strings?  
 A: Consider an electron. An electron is an elementary particle whose observed size is small enough that if it was exactly zero there would be no difference in our observations. (Except (I think?) that the implication of being point-like would mean that electrons are naked ring singularities, but as GR and QM don't play nicely together and string theory is an effort to resolve that failure, that's something I'm going to merely acknowledge and not deal with).
Despite being zero-dimensional, electrons still:


*

*Create a 3-dimensional electric force field around themselves, pulling them towards positively charged objects like protons.

*Are subject to Heisenburg uncertainty, putting them into a superposition of many possible positions. An important part of this point is that from the way they behave, electrons look like a superposition of point-like particles and not like a particle with non-zero radius.

*Are subject to certain constraints on their location, so that when they 'orbit' a proton in a certain way, the wave function describing the probability of being in any given position looks like a shell. Note that this is different from saying "the electron itself is shaped like a shell", as this is just the probability that any given observation will detect the electron in any given position. Because of the nature of these constraints, atoms can bind in interesting ways with complicated and stiff 3-dimensional structures.
For non-elementary particles such as protons and neutrons, a similar argument applies to the smaller fundamental particles that they are made from.
A: The structures of matter forms from the interaction of different fileds and not directly from the structures of elementary particles 
From the standard model of particle physics, all massive particles get their masses from the Higgs field and these masses are just energies bounded-intrinsically to the particles. Therefore all the masses we see around as is actually just the sum of elementary particles masses and potential energies of their interactions. 
The 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 a coin sized sphere then a atom would be a 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 interaction between p and e-.
If the string theory is the correct description for our universe then all the particles present in the universe are nothing but just different modes of the same fundamental 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 surrounding string. 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.
