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Among organic semiconductors, rubrene (C42H28, 5,6,11,12-tetraphenyltetracene, Rub) is extensively studied in recent years, since it exhibits interesting physical properties such as very high charge carrier mobilities in organic field-effect transistors at room temperature. Rub is used as a laser dye and as a fluorescent dopant in other organic light-emitting diodes (OLEDs) to improve the characteristics such as lifetime, stability, color, and brightness. However, there are controversies as to the Rub degradation both in the bulk state and thin layers. So, the better understanding of these phenomena is crucial for improving the performance of organic devices. In this work, we present the results on complex studies of the molecular structure, morphology, and photoluminescence (PL) of Rub layers deposited on freshly cleaved KBr(100) and Au(111) substrates by vacuum thermal evaporation. Additionally, the two-component vacuum deposited (VD) Rub-tetracene (Tc) films were studied. Special attention was paid to the susceptibility of films to the oxidation under ambient conditions. The chemical structure and molecular ordering in the obtained VD thin organic films were evaluated by FTIR spectroscopy, and the structure of the very first Rub layers on atomically smooth Au(111) surfaces was studied with scanning tunneling microscopy (STM). From the changes in the peaks position and the intensity of room-temperature PL spectra of the films with time, the degradation kinetics of the Rub emission is analyzed.