Can't speak to what you're talking about, but there are definitely well preserved examples of other organisms such as those from the Cambrian explosion in the Burgess Shales, or the fishes and archaeopteryx found in limestone. Crinoids, afaik, still exist and have existed for a long time. It is likely the ones you've seen are relatively young and we're preserved through other methods. 3D fossils typically form due to replacement of the original minerals by dissolution and then infilling by precipitation of dissolved minerals in water, or by sulphur-respiring bacteria that form pyrite in place of the original mineral.

It's been a while since I learned all of this so anyone who is up-to-date, feel free to correct me.