I am involved in materials science and not biology. However, such a fundamental question should probably be addressed in a different forum.

There is undoubtedly much written about preparing bacterial samples for EM. Please check the literature. Also, vendors in the field will often publish whitepapers on such subjects showing how their wares prove helpful. To do so, they often include plenty of details.

The answer will probably vary depending on what you are looking for. Have you determined that?

You might also ask the lab you are working with. (Have you located one yet.) They should know.