A major concern for the preparation of any kind of biological samples is usually the preservation of the structures one is interested in, without introduction of artifacts.
Unfortunately this is not always easy ... 
For X-ray fluorescence analysis of trace elements, in particular metals, in biological cells, major problems that can occur are:
- redistribution of inherent elements
- contamination with 'outside' elements
- leeching of inherent elements .
Similarily, mounting of the specimen is of importance as it not only needs to provide the specimen with support, but it has to do so without significantly increasing the fluorescence background signal.