Machining high temperature superconducting (HTS) thin films is challenging due to the material’s sensitivity. Here, 200 nm thick YBCO microbridges were machined with a femtosecond laser (300 fs at 1030 nm wavelength) as a chemical free and flexible method with minimal edge damage. Transport measurements and Raman spectroscopy were used to analyse the bridges before and after laser processing. While transport and Raman measurements are commonly used separately to evaluate YBCO, our approach links both techniques to analyse laser induced damage. The link between changes in the Raman spectrum and transport measurements is investigated by identifying changes caused by repeated heat treatments while sequentially measuring the critical current density and Raman spectra. The data obtained is used to predict critical current density losses from changes in Raman peak intensities and shifts. This technique is further investigated by applying it to laser machined YBCO bridges which were exposed to highly localised heating. Results show that for bridge widths of 10 μm, a femtosecond laser can be used to repeatedly successfully machine microbridges with no loss in critical current density and that there is some correlation to critical current changes in the Raman spectra.