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. Herein, we show 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 the population of 6-membered GeO4 rings increases at elevated substrate temperatures. Deposition near the glass transition temperature is more efficient than post-growth 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.