The characterisation of loss in optical waveguides is essential in understanding the performance of these devices and their limitations. Whilst interferometric-based methods generally provide the best results for low-loss waveguides, they are almost exclusively used to provide characterization in cases where the waveguide is spatially single-mode. Here, we introduce a Fabry-Pérot-based scheme to estimate the losses of a nonlinear (birefringent or quasi-phase matched) waveguide at a wavelength where it is multi-mode. The method involves measuring the generated second harmonic power as the pump wavelength is scanned over the phase matching region. Furthermore, it is shown that this method allows one to infer the losses of different second harmonic spatial modes by scanning the pump field over the separated phase matching spectra. By fitting the measured phase matching spectra from different titanium indiffused lithium niobate waveguides to the model presented in this paper, it is shown that one can estimate the second harmonic losses of a single spatial-mode, at wavelengths where the waveguides are spatially multi-mode.