The present invention provides methods and system for forming a buried oxide layer (BOX) region in a semiconductor substrate, such as, a silicon wafer. In one aspect, in a method of the invention, an initial dose of oxygen ions is implanted in the substrate while maintaining the substrate temperature in a range of about 300 C. to 600 C. Subsequently, a second dose of oxygen ions is implanted in the substrate while actively cooling the substrate to maintain the substrate temperature in range of about 50 C. to 150 C. These ion implantation steps are followed by an annealing step in an oxygen containing atmosphere to form a continuous BOX region in the substrate. In one preferred embodiment, the initial ion implantation step is performed in a chamber that includes a device for heating the substrate while the second ion implantation step is performed in a separate chamber that is equipped with a device for actively cooling the substrate. The annealing step can be performed in a third chamber or in either of the first or second chambers.