Isolation trenches are etched through an active silicon layer overlying a buried oxide on a substrate into the substrate, and through any pad dielectric(s) on the active silicon layer. Lateral epitaxial growth of the active silicon layer forms protrusions into the isolation trenches to a lateral distance of at least about 5 nanometers, and portions of the isolation trenches around the protrusions are filled with dielectric. Raised source/drain regions are formed on portions of the active silicon layer including a dielectric. As a result, misaligned contacts passing around edges of the raised source/drain regions remain spaced apart from sidewalls of the substrate in the isolation trenches.