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High-resolution microscope Moiré methods have recently been used to measure small deformations in specimens occasionally due to some restrictions on the use of optical measurement techniques. The atomic force microscope (AFM) Moiré method, a type of high-resolution microscope Moiré method, is usually adopted to measure the in-plane deformation of electronic packages due to the simple process of specimen preparation associated with this process. The sensitivity of the AFM Moiré method is determined by the frequency of the specimen and the reference grating. The latter is controlled by varying the pitch of the AFM scanning lines. Therefore, a high-frequency reference grating is easily achieved by decreasing the pitch. On the other hand, it is difficult to form a high-frequency specimen grating on the surface of a thin package. Alternatively, a phase-shifting technique can be employed with the Moiré method to enhance the sensitivity using a specimen grating with a relatively low grating frequency. However, some obstacles exist when doing this, including the hysteretic behavior that arises in the specimen stage actuator of the AFM system and areas mismatch among the phase-shifted images. In this paper, a pseudo-phase-shifting technique is proposed to overcome the obstacles of the AFM system. An image-decomposition algorithm that obtains phase-shifted images is also presented. For an application of the AFM Moiré method, in-plane deformations of a chip-on-flex package with thin thickness were investigated using the proposed technique. The effects of the specimen grating on the specimen were also evaluated through a finite element analysis.