Methods for providing improved isolation structures in a SiGe BiCMOS process are provided. In one method, an n-type epitaxial layer is grown over a p-type high-resistivity substrate. A mask covers a first region, and exposes a second region, of the epitaxial layer. A p-type impurity is implanted through the mask, counter-doping the second region to become slightly p-type. Shallow trench isolation and optional deep trench isolation regions are formed through the counter-doped second region, providing an isolation structure. The first region of the epitaxial layer forms a collector region of a heterojunction bipolar transistor. In another method, shallow trenches are etched partially into the epitaxial layer through a mask. A p-type impurity is implanted through the mask, thereby counter-doping thin exposed regions of the epitaxial layer to become slightly p-type. The shallow trenches are filled with dielectric material and a CMP process is performed to form shallow trench isolation regions.