FFT Background subtraction in MATLAB Using MATLAB I need to subtract the background files from the real signal I am trying to measure. We took data of just the background noise prior to driving the system with some voltage, so we do not have to estimate the background, I need to know if i can subtract the two phase wise or how I can do this with the real and imaginary parts. 

Thank you!!
I'm assuming since you didn't say that you're working with audio. But my answer generally applies if you're working with images/video as well. Unless the background you're trying to subtract is exactly the same, I doubt subtracting a phase-inverted version of the signal will work. It sounds like what you're trying to perform is spectral subtraction. This is a common technique where you simply subtract the average FFT magnitude spectrum from your signal. See this paper on spectral subtraction. If working with images/video, I assume that you could do this in 2 dimensions as well and the math would be similar.