Multimode Interference couplers (MMI) can have deviations in their amplitude and phase relations with respect to the ideal case. When using MMIs to construct a Mach-Zehnder interferometer (MZI), these deviations lead to non-ideal MZI behavior. In this paper, we introduce a correction algorithm that is able to strongly reduce amplitude and phase errors in 3 × 3 MMI based MZIs. Such MZIs are frequently used in phase estimation schemes in wavelength meters. Our method reduces the maximum phase estimation error to 2 • , as measured in fabricated devices. This is two to three times better than the conventional method by Todd et al.