[Andrés]

Sorry but you'll need 3d Studio Max to use this.

I have a saved scene with a flat grid mesh that is painted with the source picture as texture map (diffuse map) and where I apply a displace modifier (a modifier that changes height based on brightness of a texture) using the same picture (but it can be a different one).
Then all I have to do is change the source picture to render every ship.
Really easy, and it only takes a few seconds, actually cropping the original shipset into individual ships and renaming rendered results to the appropriate names takes more time than making the "pseudo-3d" part.

Now that I think about it this method can work quite fine with those fractalian "ships".
If you want, you can post or send me by email your source pics so I give them a try.
From what I remember of that fractal making program you used it can probably be interesting to try using the same source image with different color palettes to use as "diffuse map" and "elevation displace".
I don't know if you kept playing and improving that shipset after Last time I downloaded it. But another thing that IMHO your fractal shipset needs is a better differentiation of ships sizes and types. Everything looked too much the same.