In this work, we demonstrate a nanofabrication technique based on thermal scanning probe lithography (t-SPL), PDMS molding, and bottom-up capillary-assisted particle assembly (CAPA). The repeatability of the pattern transfer from the thermal sensitive polymer poly-phthalaldehyde (PPA) to PDMS is studied. Moreover, after the pattern transfer, the gold nano-rods assembly on PDMS substrates with different trap designs is also demonstrated.