In this study, we show the design and manufacturing of microfluidic deterministic lateral displacement (DLD) devices for sub-micrometer particle separation. For that purpose, devices with pillar gaps of 4 µm and a periodicity of 50 were designed. After photolithographic manufacturing of SU-8 masters with different heights (15 and 30 µm) and vertical sidewalls for soft-lithographic replication with polydimethylsiloxane (PDMS) the influence of flow rate on the separation efficiency of 0.45 and 0.97 µm particles was investigated. The 15 µm devices were operated at 0.125 and 0.5 µl/min sample flow rate and the 30 µm devices at 0.5 and 2.0 µl/min, respectively. Excellent separation efficiencies were observed for both device heights at the lower sample flow rates, while separation efficiencies decreased at the respective higher sample flow rates. The decrease in separation efficiency was attributed to deformation of the soft PDMS pillars, which causes an increase in pillar gaps at the higher sample flow rates as shown by microscopy imaging. The advantage of the 30 µm devices over the 15 µm devices is clearly shown by the separation of 0.45 and 0.97 µm particles at 0.5 µl/min. Due to reduced hydrodynamic resistance in the 30 µm devices and thus less pillar deformation, the displacement efficiency of 0.97 µm particles was above 99% compared to 46–57% for the 15 µm devices. Our 30 µm devices demonstrated excellent separation at a tenfold higher sample flow rate with 0.5 µl/min compared to comparable PDMS-based devices operating in the same size regime.