A fluorescence microscope is a light microscope used to study properties of organic or inorganic substances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption.In most cases, a component of interest in the specimen is specifically labeled with a fluorescent molecule called a fluorophore such as Green fluorescent protein, fluorescein or DyLight 488. The specimen is illuminated with light of a specific wavelength or wavelengths which is absorbed by the fluorophores, causing them to emit longer wavelengths of light of a different color than the absorbed light. The illumination light is separated from the much weaker emitted fluorescence through the use of an emission filter. Typical components of a fluorescence microscope are the light source, Xenon or Mercury arc-discharge lamp, the excitation filter, the dichroic mirror or dichromatic beamsplitter, and the emission filter. The filters and the dichroic are chosen to match the spectral excitation and emission characteristics of the fluorophore used to label the specimen. Most fluorescence microscopes in use are epi-fluorescence microscopes. These microscopes have become an important part in the field of biology, opening the doors for more advanced microscope designs, such as the confocal laser scanning microscope and the total internal reflection fluorescence microscope (TIRF). Fluorophores lose their ability to fluoresce as they are illuminated in a process called photobleaching. Special care must be taken to prevent photobleaching through the use of more robust fluorophores or by minimizing illumination.

Scanning probe microscope-
In scanning probe microscopy or SPM, a physical probe is used either in close contact to the sample or nearly touching it. By rastering the probe across the sample, and by measuring the interactions between the sharp tip of the probe and the sample, a micrograph is generated. The exact nature of the interactions between the probe and the sample determines exactly what kind of SPM is being used. Because this kind of microscopy relies on the interactions between the tip and the sample, it generally only measures information about the surface of the sample.
Some kinds of SPMs are:
• Atomic force microscope
• Scanning tunneling microscope
• Electric force microscope
• Magnetic force microscope (MFM)
• Near-field scanning optical microscope

Point Projection Microscopes-
The field emission microscope, field ion microscope, and the Atom Probe are examples of point-projection microscopes where ions are excited from a needle-shaped specimen and hit a detector. The Atom-Probe Tomograph (APT) is the most modern incarnation and allows a three-dimensional atom-by-atom (with chemical elements identified) reconstruction with sub-nanometer resolution.

Other microscopes-
Acoustic microscopes use sound waves to measure variations in acoustic impedance. Similar to SONAR in principle, they are used for such jobs as detecting defects in the subsurfaces of materials including those found in integrated circuits.