We exploit the impact of light diffraction on the morphology of silicon substrates when they are surface-structured in liquid environments using femtosecond laser pulses. This is done with the aim of applying these substrates in surface-enhanced Raman spectroscopy (SERS). Our findings demonstrate the successful creation of dome-like structures when ablating silicon substrates, while immersed in water, ethanol, and n-heptane, with a diffracted laser beam. We find that the process of creating dome-like structures is more efficient when using heptane and ethanol, and this efficiency increases as the number of line-by-line laser scans across the sample is increased. The laser ablation of Si surface in air results in forming ripples only, and the increase of scan number does not lead to domes formation. The SERS experiments on Rhodamine 6G (R6G) deposited on the laser-structured silicon substrates coated with silver nanoparticles (AgNPs) show significant enhancement of the Raman signal. Notably, the enhancement observed on surfaces featuring domed structures surpassed that seen on surfaces with ripple patterns. When evaluating R6G at a concentration of 10−9 mol/L, the presence of domes resulted in a Raman signal that was over threefold stronger.