You only need to transform the 1D array of amplitudes. You need to know the frequencies to get deltaF from which you will be able to calculate the delta time in the transform, but that is just a scaling task. You also need to know how the frequency domain data is arranged, because there are a few flavors (e.g. DC centered, Nyquist centered).
Please attach your VI with some representative data contained in a diagram constant and I'll have a look.
Don't confuse array dimensionality. A true 2D array has three dimensions: (row index, column index, value), most likely you have a 2D array with e.g. two colums, one for the amplitude and one for the frequency, so it is more like a compact representation of 2 1D arrays.