Depending on the observation methode chosen, and the goal of the observation, different preperation methodes are performed.
In transmitted light microscopy, if the sample permits this, such is the case with biological samples, a small section of the sample is extracted from its bulk. This is then further chemically and or physically treated to allow it to be cut into thin section ranging in thickness from some tens of um to as thin as 500nm. These are then further treated with chemicals (stains) to increase contrast and or differentiate certain parts of the structure from one another. Alternatively the samples my be viewed by means of interference or phase contrast. These methodes have the advantage that even living subjects my be viewed.
For Flourecence microscopy the samples are prepared as above, but treated with different stains and or antibodies to visualize proscessed within cells. Some samples exibit the ability to flourece on their own, such is the case with phosphors, or the chloroplasts in plant leafs. This flourecence can also be pumped by means of an electron beam, this is used in among other fields, mineralogy.
Sample preperation for Reflected light microscopy is somewhat simpler, allowing even the observation of surface details on the unaltered bulk sample. However, for conviniance it is usually a good idea to extract a smaller volume from the bulk sample for observation.
In the case of metals, and metal structures, it is sometimes necessery to flatten and polish the surface to be observed. this surface is further treated with an etchant to reveal, for example, the grain boundrys within bulk metals.
A somewhat rare but useful imaging methode for reflected light microscopy is the Magnetooptic Kerr microscope, which is capable of visualizing the magnetic field present at the surface of the sample. This technique can be used to, for instance, retrieve information on damaged magnetic media which is damaged to such an extent, that it is no longer readable by the playback device, or is to delicate and or valuable to risk playback with normal magnetic read heads.