Quantum information carriers with higher dimension than the canonical qubit offer significant advantages. However, manipulating such systems is extremely difficult. We show how measurement induced non-linearities can be employed to dramatically extend the range of possible transforms on biphotonic qutrits; the three level quantum systems formed by the polarisation of two photons in the same spatio-temporal mode. We fully characterise the biphoton-photon entanglement that underpins our technique, thereby realising the first instance of qubit-qutrit entanglement. We discuss an extension of our technique to generate qutrit-qutrit entanglement and to manipulate any bosonic encoding of quantum information.