Recently there has been considerable interest in developing sugar glasses that enable storage of biologics without refrigeration. Microfiber filter papers are good substrates for drying biologics in the presence of sugar glass-formers, providing for an even distribution of samples and an enhanced surface area for drying, but the opaqueness prevents macroscopic observation of the sample and can introduce complexities that impede physical characterization. Because drying kinetics and processing conditions can impact the relaxation dynamics (e.g., α- and β-relaxation), which can influence the efficacy of the glass as a stabilizer, methods are needed that can enable a determination of relaxation phenomena of sugar glasses in such complex environments. In this study we present a method which provides verification of the absence of crystallinity following drying on glass fiber filter paper and also enables the determination of relaxation characteristics of amorphous sugar compositions embedded within these filter substrates. Using material pockets to contain the sugar glass-embedded microfiber paper, the α-relaxation temperature, Tα, was determined as a function of the water content in trehalose and sucrose samples using Dynamic Mechanical Analysis (DMA). Results were verified by comparison with previous calorimetric and spectroscopic studies. The data also demonstrated the plasticizing effects of water, as Tα was shown to correlate with water content via a Gordon–Taylor-like relationship. Our findings validate a new approach for determining the relaxation characteristics of microfiber embedded sugar glasses, and offer new insights into the relaxation characteristics of glasses prepared by microwave-assisted drying on filter papers.