Functional oligosaccharides are carbohydrates that have two to ten monosaccharides units linked together with glycosidic bonds. The two linked monosaccharides (disaccharides) of maltose, sucrose, and lactose are digestible oligosaccharides by human gut enzymes. These, digestible disaccharides are sugars and are not classified as functional oligosaccharides. Functional oligosaccharides are non-digestible by human gut enzymes and providing health benefits as fibers and prebiotics [1]. The common known functional oligosaccharides are fructo-oligosaccharides, galacto-oligosaccharides, lacto-sucrose, malto-oligosaccharides, isomalto-oligosaccharides, trehalose, cyclodextrins, xylo-oligosaccharides, and soy-oligosaccharides. Two of these enzymatically produced functional oligosaccharides are cyclodextrins and trehalose. In addition, to their highlighted health benefits, both have an important pharmaceutical application in drugs delivery systems, in the case of cyclodextrins, and as cryoprotectants of biological materials, viable cells, and foods, in the case of trehalose.