A deep trench is formed in a semiconductor substrate. The deep trench may comprise a pair of parallel substantially vertical sidewalls having a constant separation distance. A set of outer substantially vertical sidewalls may have a closed shape in a horizontal cross-section. At least one dielectric layer is formed in the deep trench. The deep trench is filled with at least one conductive trench fill material to form a conductive deep trench fill region. A shallow trench isolation structure is formed directly on the deep trench to encapsulate the conductive deep trench fill region therebeneath. The stack of the deep trench and the shallow trench isolation structure form a deep trench inter-well isolation structure that provides electrical isolation of devices on one side of the stack from devices on the other side.