A 3D-FFT should be applied to a 3D-array. If you apply the 3D-FFT to a 2D-array you get the same result as a 2D-FFT, because there is no third dimension in the array.
Think about it this way: an N-dimensional FFT is just N 1-dimensional FFT's, one along each dimension. If there is no third dimension in the array, the FFT along that dimension does nothing.