We characterize the magnetic behavior of an array of magnetic bead traps based on domain walls (DWs) formed in zig-zag permalloy wires patterned on a Si substrate. Using magnetic force and magneto-optical Kerr effect microscopy, we study the nucleation and annihilation of DWs for two different wire widths. Through scanning electron microscopy with polarization analysis, we analyze in detail the magnetization configuration of the DWs in the presence of a magnetic bead previously trapped by the DW stray field. Finally, we patterned the magnetic nanostructures directly on a polydimethylsiloxane (PDMS) substrate, and we show that the functionality of the device is completely maintained. These results pave the way to the integration of DW-based devices in a PDMS lab-on-a-chip system for magnetic bead separation.