Methods for forming a trench structure with passivated surfaces. In some embodiments, a method of forming a trench structure may include etching a trench into a substrate material of the substrate, forming an oxide layer on surfaces of the trench using a dry oxide process at a temperature of less than approximately 450 degrees Celsius, selectively removing the oxide layer from surfaces of the trench, and forming a passivation layer on surfaces of the trench to form a homogeneous passivation region as part of the substrate material using a low temperature process of less than approximately 450 degrees Celsius.