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We present a cell handling method using magnetically functionalized microplates. Rectangular-shaped permalloy inside the microplates enables the plates to rotate or flip upside down by magnetic field. We conduct two kinds of cell handling experiments: (1) rotating cells for the precise positioning of cell nucleus and (2) flipping over the microplate for culturing different types of cells on both sides of the microplates. These demonstrations indicate that our handling method can be useful for single-cell-level manipulations and be a platform for a heterogeneous 3D co-culture system.