It's been a good season for fan patches! Kevin Caccamo has released version 1.5 of his Wing Blender app, previously known as Blender Commander. It allows aspiring modders to make ships in Blender and then more easily export them to Prophecy or Secret Ops. This new version adds a reverse feature where you can import a Vision Engine file to Blender to work with. You can also use this in conjunction with his MAT Viewer to more easily see your outputs as well. Grab the program and find further instructions here.
Wing Blender is an import/export script for Blender 2.65+ that allows you to export a VISION engine (Wing Commander: Prophecy, Wing Commander: Secret Ops) IFF 3D model, or import a VISION engine IFF 3D model into Blender.
This means you'll be able to do most of your work in Blender, and then simply export it to the game without having to pass the model through multiple conversion programs (3D Exploration, peoview, ModelC, etc.).
This project is the successor to OBJ2WCP, a crappy old OBJ converter written noobishly in Java.