Embodiments of present invention provide a method of making well isolations. The method includes forming a hard-mask layer on top of said substrate; forming a first resist-mask on top of a first portion of the hard-mask layer and applying the first resist-mask in forming a first type of wells in a first region of the substrate; forming a second resist-mask on top of a second portion of the hard-mask layer and applying the second resist-mask in forming a second type of wells in a second region of the substrate; applying the first and second resist-masks in transforming the hard-mask layer into a hard-mask, the hard-mask having openings aligned to areas overlapped by the first and second regions of the substrate; etching at least the areas of the substrate in creating deep trenches that separate the first and second types of wells; and filling the deep trenches with insulating materials.