A method of manufacturing FinFET semiconductor devices in memory regions and logic regions includes the steps of forming a first gate material layer on a substrate and fins, patterning the first gate material layer to form a control gate, forming a second gate material layer on the substrate and fins, performing an etch process to the cell region so that the second gate material layer in the cell region is lower than the second gate material layer in the peripheral region, patterning the second gate material layer to form a select gate in the cell region and a dummy gate in the logic region respectively.