Glasses are nonequilibrium solids with properties highly dependent on their method of preparation. In vapor-deposited molecular glasses, structural organization could be readily tuned with deposition rate and substrate temperature. Here, we show that the atomic arrangement of strong network-forming GeO2 glass is modified at medium range (<2 nm) through vapor deposition at elevated temperatures. Raman spectral signatures distinctively show that the population of six-membered GeO4 rings increases at elevated substrate temperatures. Deposition near the glass transition temperature is more efficient than postgrowth annealing in modifying atomic structure at medium range. The enhanced medium-range organization correlates with reduction of the room temperature internal friction. Identifying the microscopic origin of room temperature internal friction in amorphous oxides is paramount to design the next-generation interference coatings for mirrors of the end test masses of gravitational wave interferometers, in which the room temperature internal friction is a main source of noise limiting their sensitivity.