This paper presents a probe-based force-controlled nanoindentation method to fabricate ordered micro/nanostructures. Both the experimental and finite element simulation approaches are employed to investigate the influence of the interval between the adjacent indentations and the rotation angle of the probe on the formed micro/nanostructures. The non-contacting part between indenter and the sample material and the height of the material pile-up are two competing factors to determine the depth relationship between the adjacent indentations. For the one array indentations, nanostructures with good depth consistency and periodicity can be formed after the depth of the indentation becoming stable, and the variation of the rotation angle results in the large difference between the morphology of the formed nanostructures at the bottom of the one array indentation. In addition, for the indentation arrays, the nanostructures with good consistency and periodicity of the shape and depth can be generated with the spacing greater than 1 μm. Finally, Raman tests are also carried out based on the obtained ordered micro/nanostructures with Rhodamine probe molecule. The indentations arrays with a smaller spacing lead to better the enhancement effect of the substrate, which has the potential applications in the fields of biological or chemical molecular detection.