The etch depth during trench over via etch of a dual damascene structure in a dielectric film stack is controlled to be the same over the dense area and the open area of a substrate and solve micro-loading problems. The trench etch process is adapted to include a forward micro-loading etching process and a reverse micro-loading etching process using two etch chemistries together with the inclusion of a dopant material layer or an organic fill material layer during the deposition of the dielectric film stack. In one embodiment, etching of trenches over vias is switched from forward micro-loading to reverse micro-loading once etching of the dielectric film stack is reached at a predetermined location of a dopant material layer. In another embodiment, etching of an organic trench filling material layer is performed in a reverse micro-loading process followed by etching the dielectric film stack in a forward micro-loading process.