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Plasma-enhanced chemical vapor deposition (PECVD) is commonly used for the deposition of silica waveguide layers. When the gaps between waveguides are small, voids are created during the deposition of the upper cladding. This letter presents a new process for filling the gaps of PECVD silica waveguides using boron-germanium codoped upper-cladding and high-temperature annealing. Using appropriate doping concentrations as determined by processing gas flow rates, the image of completely filled gap was observed by scanning electron microscopy, and the measured transmission loss of an arrayed waveguide grating triplexer is reduced by about 2 dB. By avoiding the use of toxic phosphine, the proposed method has potential advantages compared with the commonly used borophosphosilicate glass process.