Silicon wafers were exposed to a cleaning sequence containing an HF etching step prior to an ammonia hydrogen peroxide mixture (APM) (or SCI) cleaning treatment. These wafers are subject to roughening according to at least three mechanisms. One roughening mechanism is due to the vapor from the,APM mixture, while the other two are strongly related to metal contamination. At first, ammonia vapor from a hot APM solution will condense an the cold hydrophobic wafer surface and will etch the surface. Second, iron-ion contamination (present as iron hydroxide aggregates in the APM), will catalyze the hydrogen peroxide decomposition. During immersion of the wafer, these iron-ion aggregates can deposit on the silicon surface. Therefore, local hydrogen peroxide depletion is created, as these aggregates continue to catalyze its decomposition. This causes local etching of the silicon in typical rings having a depth of 2-5 nm, while a rim of 3-8 nm of a silicon oxide is deposited next to the ring. Finally, metals such as copper and nickel can plate on the silicon wafer in the HF step prior to the APM step. They act as the cathode in a galvanic cell while the silicon surrounding the copper (or nickel) nuclei is dissolving anodically.