Ships and ship configuration were the topics in the most recent chat with the Star Trek Online development team.
As reported by Zam, three different types of ships will be available when the game launches. These three types will be: Escort for offense, Cruiser for general purposes and Science for deflector dish powers. There will be four tiers of ships, and sixteen different configurations of ships on the Federation side. Each will have one or two ships from canon Star Trek and the ships will be customizable.
Customization includes cosmetic things such as windows, saucers and escape pods as well as functional things, such as weapons and fields. The cosmetic changes would be done at a Starbase and the functional items can be changed in the field.
To read more, head to the article located here.