Embodiments of the invention provide a substrate processing method for bottom-up formation of a film in a recessed feature. According to one embodiment, the method includes providing a substrate containing a first layer and a second layer on the first layer, the second layer having a recessed feature extending through the second layer, and depositing a non-conformal mask layer on the substrate, where the mask layer has an overhang at an opening of the recessed feature. The method further includes removing the mask layer from a bottom of the recessed feature, while maintaining at least a portion of the overhang at the opening, selectively depositing a film on the bottom of the recessed feature, and removing the mask layer overhang from the substrate. The processing steps may be repeated at least once until the film has a desired thickness in the recessed feature.