Abstract: Provided are methods of manufacturing a three dimensional semiconductor device. The method includes providing a substrate including a cell array region and a peripheral circuit region, forming a peripheral structure on the peripheral circuit region, forming a cell structure being thicker than the peripheral structure in the cell array region, forming an interlayer dielectric to cover the peripheral structure and the cell structure, forming a polishing stop layer on the interlayer dielectric, and planarizing the interlayer dielectric using the polishing stop layer as a planarization stop.