The functional properties of magnetic tunnel junctions are critically dependant on the nanoscale morphology of the insulating barrier (usually only a few atomic layers thick) that separates the two ferromagnetic layers. Three-dimensional atom probe analysis has been used to study the chemistry of a magnetic tunnel junction structure comprising an aluminium oxide barrier formed by in situ oxidation, both in the under-oxidised and fully oxidised states and before and after annealing. Low oxidation times result in discrete oxide islands. Further oxidation leads to a more continuous, but still non-stoichiometric, barrier with evidence that oxidation proceeds along the top of grain boundaries in the underlying CoFe layer. Post-deposition annealing leads to an increase in the barrier area, but only in the case of the fully oxidised and annealed structure is a continuous planar layer formed, which is close to the stoichiometric Al:O ratio of 2:3. These results are surprising, in that the planar layers are usually considered unstable with respect to breaking up into separate islands. Analysis of the various driving forces suggests that the formation of a continuous layer requires a combination of factors, including the strain energy resulting from the expansion of the oxide during internal oxidation on annealing.