We discuss the use of Fourier transform techniques to extract layer thickness from the interference fringes observed in high resolution X-ray diffraction rocking curves of pseudomorphic HEMT structures. The interference structure is extracted by cubic spline fitting to the extrema of the data, thereby obtaining a background envelope which is used to normalise the data. The resulting constant background is subtracted from the data and the residual Fourier transformed. Auto correlation of the residual significantly improves the result from noisy data. Satisfactory results are obtained only when the Bragg peak from the substrate is windowed out. With a limited dynamic and angular range, there is often insufficient data to separate the two closely spaced periods arising from the total layer thickness and that excluding the quantum well. The result then corresponds to the average of these two thicknesses.