The formation and characteristics of micron to sub-micron size domains aligned by atomic force microscope (AFM) tip in Pb(Zr,Ti)O-3 (PZT) thin films are studied. The stability of the aligned domains is studied through the analysis of the retention characteristics. The retention time shows a linear dependence upon the size of the aligned domains. The electrical treatment of back poling is suggested to enhance the retention time and this method is proved powerful. Crystal orientation is found to take an important role in determining the retention time. As <100> oriented crystals increase, the retention time increases. The role of 90-degree domains was taken into account when explaining the phenomenon.