We studied 3D dielectrophoretic (DEP) effects induced by dielectric pillar arrays fabricated by soft lithography. Polydimethylsiloxane (PDMS) was casted onto a PMMA mold with arrays of high-aspect-ratio holes micromachined by proton beam writing (PBW), which is a novel direct-write lithographic technique using a scanning proton beam. Arrays of PDMS pillars with diameter of ∼3 µm and a height of ∼15 µm, were fabricated using the soft lithography. The 3D-DEP effect was demonstrated using the PDMS pillar arrays incorporated into a channel on a glass substrate by measuring a trapping capability of E. coli. Coupled use of the soft lithgraphy with the PBW enables us to fabricate low-cost 3D-DEP devices with improved throughput.