In the following program you'll get a glimpse at what I'm trying to do, but basically I have isolated a second harmonic function after FFT and then I need to center it and take the IFFT of it so that I can extract phase information from it. However, since I can not use negative indices the IFFT will only go from 0-+inf and I need it to IFFT the negative part of my signal. Do you guys have any suggestions on how I can accomplish this?
It sounds like you are trying to get the phase information at a specific frequency, namely the second harmonic. The FFT vi returns both magnitude and phase information versus frequency, therefore you don't necessarily need to use the FFT and the IFFT. I would recommend you look at one of the shipping examples called Amplitude Spectrum (sim).vi to get an idea how to use the FFT vi in an effective way. The example shows a simulated signal and FFT performed on it. You can also see the graphs of both the amplitude and the phase vs. frequency on separate graphs.