Methods of depositing layers having reduced interfacial contamination are disclosed herein. The inventive methods may advantageously reduce contamination at the interface between deposited layers, for example, between a deposited layer and an underlying substrate or film. In some embodiments, a method of depositing a layer may include annealing a silicon-containing layer having a first layer disposed thereon in a reducing atmosphere; removing the first layer using an etching process to expose the silicon-containing layer after annealing; and depositing a second layer on the exposed silicon-containing layer.