An old version of something I wrote once implemented a 3D grid laid out in layers, rows and columns. At each point in the grid a value was either true or false, and I used boolean to represent it. To get or set the value of a point in the 3D grid, I once coded this:
// set a single point (2, 1, 4) in the 3D space
example = false;
Watch out for nested arrays in Java (it doesn't have multidimensional arrays) - your example may look like a cuboid 3D space, but in Java boolean is an array of arrays of boolean arrays. Each individual array can have a different length.