If a race has discovered the ability to travel faster than light, without thrusting (warping space time), then they would probably be able to assemble objects out of protons/neutrons/electrons. Which is plausible. You just take waste matter, convert it to subatomic particles, then reassemble said particles to make objects. Not quite sure how it works in Star Trek (I'm not so obsessed that I know every detail!) but the above process would work.