A method to make magnetic random access memory (MRAM), in particular, perpendicular spin transfer torque MRAM or p-STT-MRAM is provided. Electrically isolated memory cell is formed by ion implantation instead of etching and dielectric refill. Oxygen ion implantation is used to convert the photolithography exposed areas into metal oxide dielectric matrix. An ultra thin single-layer or multiple-layer of oxygen-getter, selected from Mg, Zr, Y, Th, Ti, Al, Ba is inserted into the active magnetic memory layer in addition to putting a thicker such material above and below the memory layer to effectively capture the impinged oxygen ions. Oxygen is further confined within the core device layer by adding oxygen stopping layer below the bottom oxygen-getter. After a high temperature anneal, a uniformly distributed and electrically insulated metal oxide dielectric is formed across the middle device layer outside the photolithography protected device area, thus forming MRAM cell without any physical deformation and damage at the device boundary.