A uniform pattern of quantum dots and nanowires were reproducibly fabricated by creating holes in a two-layer structure using atomic force microscopy (AFM) indentation, dry-etching of polymer resists, and metal deposition through the indentation holes. The two-layer structure was created by depositing a thin gold layer onto a polymethyl methacrylate (PMMA) layer on a silicon substrate. The indentation depth was set so that the AFM tip penetrated the thin gold layer without the tip contacting the silicon substrate. This two-layer indentation was used to create a pattern of holes in the thin gold layer. Then, the PMMA was exposed to an isotropic O2 plasma etchant through the holes in the indentation pattern to form an undercut between the substrate and the gold layer. Quantum dots were subsequently created through the deposition of gold on the exposed silicon substrate through the indentation holes. Gold nanowires were also fabricated by creating indentation holes consecutively and optimizing the distance between the holes using the same two-layer indentation method. The topographic and electrical measurements of the fabricated gold nanowires suggest that our method is capable of making uniform and reproducible nanowires. The scanning electron microscopy images of the tips confirmed that the consecutive-hole-indentation method is less invasive than the conventional ploughing method, where constant tip contact occurs with the substrate during the formation of nanowires.