1. A fluorescent intensity measuring method which measures the intensity of minute points which are arranged on a substrate having a substantially flat surface and include a fluorescent substance, comprising: a first imaging step of emitting light with a wavelength with which the fluorescent substance can be excited and obtaining an image of each minute point including the fluorescent substance as a first image; a second imaging step of obtaining an image of foreign matter adhering on the substrate as a second image by light with a wavelength which does not excite the fluorescent substance; an extraction step of obtaining a binarized image by extracting a foreign matter area from the second image; and a foreign matter elimination step of disabling an image at a part overlapping the foreign matter area in the first image with the binarized image being used as a mask.