Could you explain a little bit more about your experiment? Where is the real signal coming from. What determines the timing?
LabVIEW does not have vectors. Do you mean a simple 1D array?
Do you want the single highest amplitude from each transform or the amplitudes of all frequencies that exist in each transform (well, if your input really is a pure sine wave, there should be only one frequency, right? :))
Do you only want only the amplitudes or also their location (frequency)?
How does the VI know what the "fundamental frequency" is?
Instead of doing the transforms explicitly, you could just use "extract single tone information" on the original data for example, and grab the amplitude output only. Also, if you know the number of desired samples beforehand (and there is no need to be able to prematurely interrupt), use a FOR loop. Just autoindex the amplitudes at the right loop boundaries to form an array.