There is a specific d20 Traveller called T20 or something, but Mongoose Traveller is much closer to Classic Traveller than anything D20. You could say both are just versions of the same thing really.
Basically transfering from CT to mongoose will be quite simple allthough not immediate (differences include non lethal char gen, less skills, etc, but the char gen notably keeps the same structure as good ol'Traveller)
So if you allready have CT, you have the fluff elements for Alien (which should not change), and for appropriate rules (char gen) you will need to adapt a bit the CT char gen, giving skills in same way as mongoose (basically less skills), adding maybe events, etc, while you wait for Mongoose version of Alien books (but by then you may decide not necessary for you).