the spot in microchip is quite small, so I guess fluorescence data in 96-well plates after being detected by Fluorescence Detector also need to be corrected using some ways of data handling
It is always a good idea to measure the background signal from another well in which the fluorescent substance has been omitted. This background can then be subtracted.
If you are trying to measure the fluorescence from a small solid object in the well, you should use a plate reader that is capable of sampling from multiple positions within the same well, to make sure the object is detected.