1)create you model in your favorite 3d program - export as a obj(seems the 3ds import for magic 2 is broken)
2) import your model into magic - assign your textures - export as a mag
3) extract the build def you wish to replace
4) create in starshatter root dir the folders ships/buildings
5) place all relevant files there - edit the def to refer to your model and your done
This will replace all instances of that building throughout the game.
I replaced the admin building here.

You can download it from grouper