Abstract: This invention is about a method to make magnetic random access memory with small footprint directly on CMOS VIA with a self-aligned etching process. The process schemes of the method proceeds as: (1) Etch MTJ and BE using one or more of RIE and/or IBE processes with Ta as hard mask; (2) Etch BE using one or more of RIE and/or IBE processes with Ta & sidewall protection layer on MTJ as hard mask; and (3) Etch a part of MTJ and BE using one or more of RIE and/or IBE processes with Ta & sidewall protection layer on top portion of MTJ as hard mask. All the three schemes lead the BE to be self-aligned to MTJ cells, the photo overlay margin is not necessary and circuits could be made extremely small with lower manufacturing cost; The invention also provides schemes to prevent the electrical shorting across the tunnel barrier layer. Through trimming and sidewall protection deposition process, device performance and electrical/magnetic properties could be greatly improved.