Embodiments provide methods for etching and depositing silicon materials on a substrate. In one example, the method includes heating a substrate containing a silicon-containing material to a temperature of about 800° C. or less and removing a portion of the silicon-containing material and a contaminant to reveal an exposed surface of the silicon-containing material during an etching process and depositing a silicon-containing layer on the exposed surface of the silicon-containing material during a deposition process. The method further provides conducting the etching and deposition processes in the same chamber and utilizing chlorine gas and a silicon source gas during the etching and deposition processes. In some examples, the silicon-containing material is removed at a rate within a range from about 2 Å per minute to about 20 Å per minute during the etching process.