If you're looking to model, you could try Blender.
There was a post last week by Treewyrn, about MaxLancer. He made some bits and bobs for 3ds Max specifically to help with Freelancer modding. Could be worth looking into.
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Yeah Blender is what I see most people using to model ships. But I do not know if they use the same programme to add animation and hard points, pretty sure that's a different programme they use for that.