Although, there are several research studies on the engineering of the graphene layers using different etching techniques, there is not any comprehensive study on the effects of using different etching masks in the reactive ion etching (RIE) method on the quality and uniformity of the etched graphene films. This study investigated the effects of using polystyrene and conventional photolithography resist as a etching mask on the engineering of the number of graphene layers, using RIE. The effects were studied using Raman spectroscopy. This analysis indicated that the photo-resist mask is better than the polystyrene mask because of its lower post processing effects on the graphene surface during the RIE process. A single layer graphene was achieved from a bi-layer graphene after 3 s of the RIE process using oxygen plasma, and the bi-layer graphene was successfully etched after 6 s of the RIE process. The bilayer etching time was significantly smaller than reported values for graphene flakes in previous research.