reshape() the data to 256,256,256 . You might then have to permute() the data to get the order right, depending on the order the inputs were in. MATLAB stores data down columns first. Keep in mind that MATLAB normally uses row as the Y coordinate, column as the X coordinate, and the third dimensional as Z.
Once you have the data in the cube arrangement you want, you can permute and reshape to form 256 * 65536 arrays, or you can extract slices corresponding to constant X, Y, or Z, or you can use slice() to get some stranger extracted data.