Specifically, the scientists started with two parallel gold nanostructures on a silicate substrate. Those structures were formed by electron-beam lithography, one of several widely used nanoscale construction techniques limited to making structures tens of nanometers or larger. Layers of organic molecules then were applied atop the initial structures to make them bigger and wider, at the same time reducing the gap between the structures. Imagine two cookies rising beside each other while baking, with the space between the cookies getting smaller as they cook, and you get a sense of how each of the initial structures grows by the addition of organic molecules and how the space between the structures gets narrower. Because the scientists knew the size and spacing of the initial structures and the thickness of the layers of films created by the molecules atop the structures, they could calculate the size of the narrowing space between the structures.
Scientists use the resulting space for forming even smaller wires by filling the space with gold.
For their research, the scientists used silicate as the substrate, gold for the prefabricated initial structures, and mercaptoalkanoic acid as the organic molecule. We know how to make the ends of organic molecules so that they bind selectively, both to each other and to the substrate. We also know they form films when they interact, and from that we can determine a precise thickness of the film. That's what makes the whole thing work. If they did not do that, the process would be just as crude as the standard polymer resists.