Methods for chemical mechanical planarization of patterned wafers are provided herein. In some embodiments, methods of processing a substrate having a first surface and a plurality of recesses disposed within the first surface may include: depositing a first material into the plurality of recesses to predominantly fill the plurality of recesses with the first material; depositing a second material different from the first material into the plurality of recesses and atop the substrate to fill the plurality of recesses and to form a layer atop the first surface; and planarizing the second material using a first slurry in a chemical mechanical polishing tool until the first surface is reached. In some embodiments, a second slurry, different than the first slurry, is used to planarize the substrate to a first level.