It can be done. Adding one of the Star Trek models into, say the Freespace 2 folder requires a few things:
Ship model, which goes into the data/models folder
ship textures, which go into the data/maps folder
a properly formatted modular table file for the ship, which goes into the data/tables folder
Be advised however, that if you are using one of the existing models/maps/table files as source, they will probably reference custom weapons as well, in that case, you'll also need:
Weapon model (if were talking about something like a torpedo)
Weapon model textures (same 'if')
Weapon effects for primaries, which go into the data/effects folder
a properly formatted modular weapons table file, which again goes into the data/tables folder.
There may also be glow-point textures referenced by the weapon and ship models, which go into the effects folder (IIRC).
Finally, take note that even if you successfully add such model or models alongside the FS2 models, they won't show up in any missions. You'd need to open the missions in FRED and add them in, but this would likely unbalance the mission, so it is not recommended. The more likely option is if the ships you are adding in are player-flyable, so you could choose to fly them in place of the FS2 ships. Be advised, however, that in order to do that, and use them in the campaign, you'd need to also edit the mission files and possibly the campaign file, in order to make the ships and weapons, accessible to the player. Otherwise, they won't show up in pre-flight.