A magnetic tunnel junction (MTJ) with direct contact is manufactured having lower resistances, improved yield, and simpler fabrication. The lower resistances improve both read and write processes in the MTJ. The MTJ layers are deposited on a bottom electrode aligned with the bottom metal. An etch stop layer may be deposited adjacent to the bottom metal to prevent overetch of an insulator surrounding the bottom metal. The bottom electrode is planarized before deposition of the MTJ layers to provide a substantially flat surface. Additionally, an underlayer may be deposited on the bottom electrode before the MTJ layers to promote desired characteristics of the MTJ.