A method for making a semiconductor device may include forming, above a substrate, a plurality of laterally spaced-apart semiconductor fins, and forming regions of a first dielectric material between the laterally spaced-apart semiconductor fins. The method may further include selectively removing at least one intermediate semiconductor fin from among the plurality of semiconductor fins to define at least one trench between corresponding regions of the first dielectric material, and forming a region of a second dielectric material different than the first dielectric in the at least one trench to provide at least one isolation pillar between adjacent semiconductor fins.