Please explore the "fft" command in Scilab. Since your data will most likely be aperiodic, see a similar discussion here.
Also, Octave has a "signal" package that facilitates many signal processing functions that could come handy to you. As a matter of fact, we also have a scilab-octave toolbox which can be downloaded from here. Using this toolbox, all of the "signal" package functions can be easily called from scilab.