Hyper cubes are created when 5 jewels of the same color are lined up in a row - the achievement will unlock once you exit the game in which you create your 1000 hyper cube. If you are trying to set them up, it is easier to set them up in columns (vertically) rather than horizontally due to the rows potentially shifting unevenly.
Through normal gameplay and Endless Mode, you should easily receive this by the end of the 280 levels needed for that achievement. You can check your progress by clicking on "Leaderboards" on the main screen.