The surface kinetics of reactive molecular beam scattering have been analyzed by discrete Fourier analysis of the scattered product waveform. In experiment and by calculation, it has been shown that with square wave modulation, harmonics in the scattered waveform as high as 29 can be significant. These harmonics can be used to characterized the transfer function of linear surface kinetics with modulation at four or fewer frequences. Optimum signal-to-noise in the derived rate parameter is obtained using the phase shift of the first harmonic where K/ω is approximately one. Fourier waveform analysis of square wave modulation compares favorably with lock-in amplifier detection, cross correlation modulation, and pulse testing for the analysis of surface kinetics.