Tunnel magnetoresistance (TMR) ratio as a function of annealing temperature for ferromagnetic tunnel junctions prepared using different oxidation methods was measured. The junction with plasma oxidation showed a TMR ratio of 31% before heat treatment and it increased to 49% after annealing at 300°C. On the other hand, the TMR ratio for the junction with radical oxidation showed a maximum at 350°C. The difference of thermal stability originates from the different oxidation procedure. The initial oxidation process of thin aluminium films was investigated by scanning tunnelling microscopy (STM). The STM images revealed progression of oxygen penetration into an aluminium film composed of small grains. Oxygen first covered the aluminium grain surface homogeneously for the plasma-oxidized junction; then oxygen inserted into the aluminium grain boundaries selectively for the radical-oxidized junction.