We have developed the inverted microstrip line photonic bandgap (IML-PBG) structure using the surface micro-machining technology on the high resistivity silicon (HRS) substrate. Because, when the IML was fabricated, the holes for removing a sacrificial layer were necessary, we have introduced these holes into the PBG structure for the Ku-band stop filter (BSF). Rectangular spiral PBG structure showed the notch characteristics and the array with suitable distance showed the stop band with under - 20 dB from 15 to 19 GHz and under - 3 dB pass-band loss.