Fluorescent dyes are often used to stain molecules within a cell. The stained cell can then be viewed under a fluorescence microscope to produce an image of the cell and allow you to distinguish between the different molecules in that cell. Two examples of commonly used fluorescent dyes are fluorescein and rhodamine. If fluorecein gets excited by blue light then it will emit an intense green colour and rhodamine will emit a deep red colour if it gets excited by green-yellow light waves. You can stain two different molecules within the same cell with two different fluorescent dyes for example you could use both fluorescein and rhodamine. You can then visualise where these molecules are within a cell compared to each other by using different filters in the fluorescent microscope which are specific for each of the dyes being used. If you attach more fluorescent dyes to different molecules in a cell then you can build up an image of the cell and distinguish between the different types of molecules with in that cell. Some newer dyes have been developed such as Cy3, Cy5 and alexa dyes, however, these dyes need a very specific wavelength to be excited and fluoresce. Their colour also fades quickly if they are illuminated too many times under the microscope.
Alberts, B. et al.(2008) Molecular Biology of the Cell. 5th edition. New York: Garland Science