Laser-written waveguides in glass have many potential applications as photonic devices. However, there is little knowledge of the actual profile of the usually asymmetric refractive index (RI) change across the femtosecond (fs) laser-written waveguides. We show, here, a new nondestructive method to measure any symmetric or asymmetric two-dimensional RI profile of fs laser-written waveguides in transparent materials. The method is also suitable for the measurement of the RI profile of any other type of waveguide. A Mach-Zehnder interferometer is used to obtain the phase shift of light propagating transversely through the RI-modified region. A genetic algorithm is then used to determine the matching cross-sectional RI profile based on the known waveguide shape and dimensions. A validation of the method with the comparison to a RNF measurement of the industry-standard SMF-28 is presented, as well as a demonstration of its versatility with measurements on fs laser-written waveguides.