I am now a lvl 50 so I can buy and use any ship, but I was wandering is it possible to create my own ship in a 3rd party 3d design program, and add it to the game (useing the specs of an already purchased ship)?

No. At this time you can only use existing ships.

It would be nice to have option to create your own new ship from previous ships parts, it could be new option for foundry.

One of the proposed Ship ugrades is to have more design choices and the ability to Craft your own ships. That will come after Fleet-bases, though.

And that means not very fast, if ever.

Cosmic is right, at best it will be new options or new ship varients which we can use to change the look of our ship.

But we will never see fanmade designs outside of contests due to legalities such as licensing and copyright issues. Not to mention CBS having to go through their approval process.