An information processing apparatus includes management circuitry that manages three-dimensional data obtained by a scanner in the order of obtaining, display controller circuitry that controls a display to show a three-dimensional image generated from combined data generated by combining a plurality of pieces of three-dimensional data, and input circuitry that accepts an operation by a user. When the input circuitry accepts an operation to select three-dimensional data, the management circuitry sets, from the selected three-dimensional data of last obtained three-dimensional data, data to be deleted. The display controller circuitry controls the display to show a three-dimensional image modified to exclude the data to be deleted.