We present two methods based on the analysis of Fabry-Perot interference for a detailed characterization of a 90degrees corner in a two-dimensional photonic crystal waveguide fabricated in a thin Si membrane. These methods are a means of identifying the critical waveguide elements in the process of improving photonic crystal devices. The effects of the elements forming the photonic crystal waveguide are identified and quantified by means of a stage-by-stage analysis. By Fourier transforming the transmission spectra we observe the amount of light that is back reflected inside the waveguide and based on the fringe contrast of the Fabry-Perot modulation we calculate the loss contribution of each waveguide element, such as the tapers and the 90degrees corner.