A method includes forming a first pad oxide layer and a second pad oxide layer over a first active region and a second active region, respectively, of a semiconductor substrate, forming a dielectric protection layer overlapping the first pad oxide layer, removing the second pad oxide layer, and forming a floating gate dielectric over the second active region. A floating gate layer is then formed to include a first portion over the dielectric protection layer, and a second portion over the floating gate dielectric. A planarization is performed on the first portion and the second portion of the floating gate layer. A blocking layer, a control gate layer, and a hard mask layer are formed over the second portion of the floating gate layer. The hard mask layer, the control gate layer, and the blocking layer are patterned to form a gate stack for a flash memory cell.