Protrusive defects on the color filter of thin-film transistor (TFT) liquid crystal displays (LCDs) frequently damage the valuable photomask. An fast method using side-view illuminations associated with digital charge-couple devices (CCDs) to detect the protrusive defect in the four substrates, which are the black matrix (BM), red, green, and blue. Between the photomask and substrate, the depth of field (DOF) is normally 300 μm for the proximity-type aligner; we select the four substrates to evaluate the detectability in the task. The experiment is capable of detecting measurements of 300 μm and even lower than 100 μm can be assessed successfully. The maximum error of the measurement is within 6% among the four samples. Furthermore, the uncertainty analysis of three standard deviations is conducted. Thus, the method is cost-effective to prevent damage for valuable photomasks in the flat panel display industry.