Intro Question to Signal Processing (Low-Pass Filter)
Based on your description it sounds like the idea is to use the FFT to figure out where your signal energy is in terms of frequencies.  Once you know that you know what the passband of your filter should be, and from that you can decide on a reasonable cutoff frequency.  You want to cutoff as much of the noise energy as possible which means you want to have the cutoff frequency as close to the passband frequency as possible, but you need some space for the transition band to make the filter implementable with a reasonable number of taps.

By the way, I often like to look at the signal energy in the log scale because it helps to get a better understanding of the weaker portions of the signal.  In Matlab you do it like so:

plot(20*log10(abs(fft(signal))))