Not as much as you would think. Conodonts are composed of calcium phosphate -- the same stuff as our teeth. It's fairly durable mineral. They are usually extracted from rocks in almost unaltered state. Conodonts do get broken and worn like any other sediment particle, so sometimes they're a bit beaten up, but often they are nearly intact despite being fairly fragile-looking structures. Sometimes their surfaces even show wear from the time when the animal was alive (i.e. tooth wear). Growth lines and other structures are visible internally.
The rest of the animal -- the body -- is soft tissues, so that part rarely preserves and is flattened even when it is preserved, however, multiple specimens compressed in different orientations reveal the 3D structure. There are also slightly more robust structures around the eye sockets (sclerotic capsules).
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