In-situ thermal anneal and substrate biased radio frequency plasma treatments are chosen to smooth the bottom electrode prior to the deposition of the AlOx barrier and the top electrode in the bottom pinned magnetic tunnel junctions (MTJs) stackes. Atomic force microscopy images indicate that surface roughness could be reduced by low energy plasma etching (40 W) on the in-situ heated bottom electrode. The tunnel magnetoresistance (TMR) and ferromagnetic interlayer coupling (H-in) behaviors versus ex-situ anneal temperature for treated and untreated junctions are studied. The results indicate that magnetic tunnel junctions deposited on the smoothed electrode show good thermal stability, high TMR signal, low interlayer coupling field, and sharp magnetization reversal of the free layer. It is concluded that the interface roughness is of great importance and must be well controlled in order to obtain high performance MTJs. (c) 2006 Elsevier B.V. All rights reserved.