A fabrication technique is proposed based on tip-based ultrasonic vibration-assisted scratching (UVAS) combined with wet chemical etching. UVAS induced a deeper subsurface damage of the machined nanostructure than the conventional scratching (CS), obtaining a high depth-to-width ratio nanostructure after hydrofluoric acid etching. Furthermore, the tip wear for UVAS was lesser than that for CS owing to the small friction of UVAS. Furthermore, periodic nanograting structures, nanodot arrays, and chiral nanostructures were machined by controlling the UVAS trajectory. Moreover, surface-enhanced Raman scattering (SERS) substrates with nanodot arrays and chiral structures were prepared based on the transferred polydimethylsiloxane (PDMS) model after Au deposition. It was found that a large depth-to-width ratio SERS substrate contributed to a high enhancement of the Raman signal. A maximum enhancement factor of 4.03 × 105 could be obtained on an optimal nanodot array SERS substrate when measuring 10–5 mol/L rhodamine 6G (R6G). The circular dichroism (CD) spectra of the chiral nanostructures were revealed through the finite element method simulation. Moreover, the multipole resonance led to the CD enhancement of the chiral nanostructures. Furthermore, the chiral enantiomers (l- and d-cysteines) were tested with the SERS-active chiral nanostructures, which can be recognized using the chiral SERS substrates directly. Thus, the proposed method showed great potential in chiral applications such as chiral sensing and label-free detection.