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Rutile germanium oxide (r-GeO2), an ultrawide bandgap semiconductor, is a promising material for next-generation power electronics. Understanding and controlling the structure and morphology of r-GeO2 thin films are crucial for advancing their integration into future devices. In this work, r-GeO2 thin films were grown using RF magnetron sputtering on r plane sapphire substrates. Postdeposition annealing (PDA) was performed in an oxygen ambient atmosphere to crystallize the films. PDA at 950 °C resulted in the formation of needle-like nanostructures, predominantly originating at the edges of the film and growing inward toward the sample center. Sequential annealing at increasing temperatures indicated that these needle-like structures begin forming at temperatures above 925 °C. Next, the effect of the PDA duration on the structure was studied. It was seen that PDA at 950 °C for durations of 1 to 15 min promoted formation of the rutile phase, and extending the PDA duration allowed greater surface coverage of the nanostructures. However, annealing even longer, i.e., for 120 min, resulted in mixed phases of α-quartz and rutile GeO2. These findings demonstrate that controlling the PDA temperature and duration can effectively modulate the morphology of rutile-phase GeO2 thin films.