A method of forming an integrated deep and shallow trench isolation structure comprises depositing a hard mask on a film stack having a plurality of layers formed on a substrate such that the hard mask is deposited on a furthermost layer from the substrate, imprinting a first pattern into the hard mask to define an open end of a first trench, imprinting a second pattern into the hard mask to define an open end of a second trench, and etching into the film stack the first trench to a first depth and the second trench to a second depth such that the first trench and the second trench each define a blind aperture in the surface of the film stack.