Whether you are looking to craft your matrix cube or to disassemble it, you will need to go to Dromund Kaas in the "Black Temple Access" area:
To assemble your matrix cube, you will first need to equip yourself with your three matrix crystals. Place them in the receptacles and then start manufacturing with the central machine. Find all the possible combinations in this article.
Then click on the cube to get it, it will slip into your inventory in the "Mission Objects" tab, it is unique and as long as you have it you will not be able to craft any other cubes, in order to create a new cube you must first disassemble the old one.
To disassemble your cube you will first need to go to Tatooine in Mos Ila and purchase a "Reconfigured Disassembly Core" from the merchant Jawa Pitkth (628; 2785) for the sum of 8000 credits. Then go back to Dromund kaas in the old assembly room and use the machine on the side to disassemble your cube, you will collect your shards and be able to craft a new one.