An array of “mushroom” style phase change memory cells is manufactured by forming a separation layer over an array of contacts, forming an isolation layer on the separation layer and forming an array of memory element openings in the isolation layer using a lithographic process. Etch masks are formed within the memory element openings by a process that compensates for variation in the size of the memory element openings that results from the lithographic process. The etch masks are used to etch through the separation layer to define an array of electrode openings. Electrode material is deposited within the electrode openings; and memory elements are formed within the memory element openings. The memory elements and bottom electrodes are self-aligned.