The process of pseudomorphism may be mechanical, structural, or chemical in nature and results from changes in the physical and chemical environment during or after the period of initial crystallization. A pseudomorph is classified both by the nature of the processes by which it was formed and by the changes it experienced during those processes. Three mechanisms of pseudomorphism can be defined as:

Substitution

In this mechanism chemical constituents are simultaneously removed and replaced by other chemical constituents during alteration. An example is the replacement of wood fibers by quartz to form petrified wood that has the outward appearance of the original wood, but is composed of quartz. Another example is the alteration of fluorite which forms isometric crystals and is sometimes replaced by quartz during alteration. The resulting quartz crystals look isometric, and are said to be pseudomorphed after fluorite.

Encrustation

If during the alteration process a thin crust of a new mineral forms on the surface of a preexisting mineral, then the preexisting mineral is removed, leaving the crust behind, we say that pseudomorphism has resulted from encrustation. In this case the thin crust of the new mineral will have casts of the form of the original mineral.

Alteration

If only partial removal of the original mineral and only partial replacement by the new mineral has taken place, then it is possible to have a the space once occupied entirely by the original mineral be partially composed of the new mineral.

The pseudomorphic change is expressed, for example, as "aragonite (original mineral) > calcite (later mineral)." Another way of writing it is "calcite after aragonite."