Proton beam writing (PBW) was applied to the fabrication of dielectrophoretic (DEP) devices equipped with high-aspect-ratio pillar arrays. With coupled use of soft lithography for micro-fluidic channels, we successfully fabricated a device equipped with SU-8 pillar arrays produced by PBW, which is covered with a poly-dimethylsiloxane (PDMS) micro-fluidic channel. For more simplified prototyping of the device, we modified a SU-8 mold for simultaneous replication of both pillar arrays and micro-fluidic channel on PDMS. Replication of pillar arrays is limited to the aspect ratio of less than three.