A process flow for forming a magnetic tunnel junction (MTJ) cell that is self-aligned to an underlying bottom electrode (BE) is disclosed. The BE is comprised of a lower BE layer having a first width (w1), and an upper (second) BE layer with a second width (w2) where w2>w1. Preferably, the BE has a T shape. A stack of MTJ layers including an uppermost hard mask is deposited on the BE and has width w2 because of a self-aligned deposition process. A dummy MTJ stack is also formed around the first BE layer. An ion beam etch where ions are at an incident angle