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Using model-based infrared reflectometry (MBIR) technique [1] we have developed a method for in-line process monitoring of polyimide passivation films to support the fabrication of fine pitch flip chip devices. A permanent passivation layer is incorporated in semiconductor wafers before the addition of solder in flip chip interconnects to protect sensitive on-chip components from chip-package interconnection (CPI) stresses, the egress of moisture and chemicals, while providing dielectric isolation. Photosensitive Polyimide (PSPI) [2] is often selected for this application because of its well established track record coupled with thermal and chemical stability, and mechanical strength. With the advent of 3-D integration technologies, new attention has been focused on creating options for reducing controlled collapse chip connection (C4) pitch and solder volumes, a change which causes co-planarity of the interconnect and the passivation layer which supports it to play an increasingly important role. An accurate in-line characterization method is needed to monitor and reduce variability in polyimide passivation layer thickness. We have developed an in-line metrology process utilizing MBIR tools which provide valuable wafer level thickness characterization of PSPI films on bare and processed 300 mm Si wafers.