Abstract Magneto-static stray field ( H stray ) interactions become an important issue when perpendicular CoFeB/MgO magnetic tunnel junctions (MTJs) are miniaturized. This raises the issue of which of the two mainstream etching processes, the pillar structure and the step structure, is better able to retain MTJ performance at extremely small scales. In the current study, we first simulated H stray effects as a function of Ruderman–Kittel–Kasuya–Yosida strength within a synthetic antiferromagnetic structure for the two structures. Our results revealed that H stray interactions were less influential (in terms of offset field) in step MTJs than in pillar MTJs during MTJ miniaturization. This is in good agreement with experimental results. This finding is further supported by adding Dzyaloshinskii–Moriya interactions into the free-layer of the two structures. We further simulated thermal stability with the inclusion of H stray for 30 nm MTJs. We found that adding etching damage effects (i.e. assuming both anisotropy constant and saturation magnetization of the free layer had some degree of loss) into the model of the pillar MTJ was necessary to obtain a trend that is close to the experimental results of thermal stability. This information can provide some guidance on the technical choices for the MTJ miniaturization.