The crystallization structure and thickness of PtMn layer in a magnetic tunnel junction system are important factors to improve its exchange bias effect. This study shows that the PtMn layer could be changed from a FCC (111) structure to a FCT (111) structure after annealing above 270°C. The minimum thickness of PtMn layer is found to be 10 nm for exchange coupling effect to be occurred in our MTJ system. The magnetic exchange effect between PtMn and SAP layers is near 4,300 Oe. Annealing temperatures can be higher than 400°C for samples without patterning; however, temperature at 275°C is too high for samples after patterning. This may be due to the breakdown of edges of the patterned samples as well as the complicated environments around the patterned samples.