A capacitor and an NVM cell are formed in an integrated fashion so that the etching of the capacitor is useful in end point detection of an etch of the NVM cell. This is achieved using two conductive layers over an NVM region and over a capacitor region. The first conductive layer is patterned in preparation for a subsequent patterning step which includes a step of patterning both the first conductive layer and the second conductive layer in both the NVM region and the capacitor region. The subsequent etch provides for an important alignment of a floating gate to the overlying control gate by having both conductive layers etched using the same mask. During this subsequent etch, the fact that first conductive material is being etched in the capacitor region helps end point detection of the etch of the first conductive layer in the NVM region.