Anything that supports separate layers of colour would do nicely, but on the cheap, you could just use paint (or whatever you used) and leave the background black, rather than cyan.
Save, then do a floodfill of colour in the background to find the non-pure-black spots you want to get rid of.
OK looks like Alpha Kodiak will be the one helping me with the AI for this race. I'll continue to post the shipset as it comes along. Any criticsms or advice from anybody on the ships are welcome