A bonded assembly of a first wafer including a first semiconductor substrate and a second wafer including a second semiconductor substrate may be formed. The second semiconductor substrate may be thinned to a first thickness, and an inter-wafer moat trench may be formed at a periphery of the bonded assembly. A protective material layer may be formed in the inter-wafer moat trench and over the backside surface of the second semiconductor substrate. A peripheral portion of the second semiconductor substrate located outside the inter-wafer moat trench may be removed, and a cylindrical portion of the protective material layer laterally surrounds a remaining portion of the bonded assembly. The second semiconductor substrate may be thinned to a second thickness by performing at least one thinning process while the cylindrical portion of the protective material layer protects the remaining portion of the bonded assembly.