The ships aren't mine. The FAQ is
First question is what exactly are you trying to do? Are you trying to add the ships from the star trek mod to the game and then FRED a mission with them in?
Adding a ship is a three step process really.
1) Make the new ships model in pof format. (If you're using a mod this part should have been taken care of for you). If you want to use ships not in the mod already you'll have to make them yourself or wait for someone like Omniscaper or Robo Getter G to get around to them. If you want to try your hand at making your own ships click on the link to my FAQ below but this time go to the modding section.
2) Edit the ships.tbl and weapons.tbl so that freespace knows how to use the model. (The Star Trek mod may or may not have done this for you. I'm not certain because I've never tried it). If the table files aren't done for you again you have to wait or learn to table edit yoursefl. It's not a hard skill to learn.
This tutorial will give you all the help you need to get started.
3) Make a new mission using the new model or edit an existing one to use it. For that bit you need the link to the FRED section of my FAQ that Goober gave you earlier.