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The empty spaces within an organism (spaces filled with liquid or gas during life) become filled with mineral-rich groundwater.

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Paleontology is the study of fossils: their age, method of formation, and evolutionary significance.In this case the fossil consists of original material, albeit in a geochemically altered state.This chemical change is an expression of diagenesis.A shell is said to be recrystallized when the original skeletal compounds are still present but in a different crystal form, as from aragonite to calcite.Compression fossils, such as those of fossil ferns, are the result of chemical reduction of the complex organic molecules composing the organism's tissues.This process can occur in very small spaces, such as within the cell wall of a plant cell.

Small scale permineralization can produce very detailed fossils.

If this happens rapidly before significant decay to the organic tissue, very fine three-dimensional morphological detail can be preserved.

Nodules from the Carboniferous Mazon Creek fossil beds of Illinois, USA, are among the best documented examples of such mineralization.

Replacement occurs when the shell, bone or other tissue is replaced with another mineral.

In some cases mineral replacement of the original shell occurs so gradually and at such fine scales that microstructural features are preserved despite the total loss of original material.

If this hole is later filled with other minerals, it is a cast.