Abstract In this study, we fabricated laser-induced periodic surface structures (LIPSS) on a germanium surface through laser ablation in air using axicon and femtosecond (fs) pulses. This novel approach permitted the nanoscale material processing outcome refinement via an fs Bessel beam. Our investigations aimed at systematically understanding the formation of periodic structures under various experimental conditions, such as (i) different pulse energies ranging from 50 µJ to 1000 µJ at a constant scan speed and (ii) constant energy with different scan speeds (0.1–3 mm s−1). By adjusting the fluences and scan speeds, we were able to identify the parametric space and alter the periodicity of the low-spatial frequency LIPSS and high-spatial frequency LIPSS on germanium, which were analyzed using field emission scanning electron microscopy. An optimal LIPSS formation over a large area of germanium was achieved at an input energy of 250 µJ and a scan speed of 0.75 mm s−1. Additionally, we measured the contact angles of the Ge nanostructures (GeNSs) to demonstrate their hydrophobic nature and non-wetting properties, providing insights into the behavior of LIPSS. Subsequently, the GeNSs were coated with a ∼15 nm thick gold (Au) film using a thermal deposition method. Utilizing these, the surface-enhanced Raman spectroscopy (SERS) technique detected diverse analytes, such as tetryl (an explosive) at a concentration of 50 µM and thiram (a pesticide) at 500 nM. The SERS enhancement factors for tetryl and thiram molecules on GeNSs coated with a 15 nm-thick Au layer were determined to be 2.5 × 104 and 4.2 × 105, respectively.