Methods and systems for detecting pinholes in a film formed on a wafer or for monitoring a thermal process tool are provided. One method for detecting pinholes in a film formed on a wafer includes generating output responsive to light from the wafer using an inspection system. The output includes first output corresponding to defects on the wafer and second output that does not correspond to the defects. This method also includes detecting the pinholes in the film formed on the wafer using the second output. One method for monitoring a thermal process tool includes generating output responsive to light from a wafer using an inspection system. The output includes the first and second output described above. The wafer was processed by the thermal process tool prior to generating the output. The method also includes monitoring the thermal process tool using the second output.