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A combination of analytical techniques, with special emphasis on selective area Stokes polarimetry, has been used to explore the structural properties and magnetic behavior of focused ion beam patterned Fe thin films under controlled Ga+ ion irradiation. Ion irradiation at doses ranging from 7.7 × 1015 to 5.2 × 1016 Ga ions cm-2 did not noticeably alter the chemical properties of the Fe, but changes to the film structure and increased coercivity were observed even after the lowest doses. Magnetic transmission x-ray microscopy provided detailed information about the magnetization reversal process occurring within a patterned area of film comprising both Fe and Fe-Ga regions, and clearly showed domain wall pinning around the magnetically harder Fe-Ga.