Cells rapidly undergo cell division during the embryogenesis. Such dynamic behaviors of cells during the embryogenesis are considered to be strongly associated with their mechanical properties such as cell-cell mechanical interactions and cell stiffness. However, the interplay between the morphogenesis and the mechanical property of whole cell assembly during the developmental process has not been well understood. To exploring the mechanism of forming the whole cell assembly, we proposed atomic force microscopy (AFM) combined with a microarray technique, which allows us to map mechanical property of the whole cell assembly. In this AFM setup, the cell assembly is randomly directed in the microarray well, and thus the average mechanical property of the whole cell assembly can be reconstructed from mapping images obtained from different cell assemblies.