Using the focused ion beam (FIB) to prepare plan-view transmission electron microscopy (TEM) specimens is beneficial for obtaining structural information of two-dimensional atomic layer materials, such as graphene and molybdenum disulfide (MoS2) nanosheets supported on substrates. The scanning electron microscopy (SEM) image in a dual-beam FIB-SEM can accurately locate an area of interest for specimen preparation. Besides, FIB specimen preparation avoids damages and hydrocarbon contamination that are usually produced in other preparation methods, in which chemical etching and polymer adhesion layers are used. In order to reduce harmful ion-beam bombardment and re-deposition on the thin atomic layers during FIB specimen preparation, we develop a method to protect the atomic layers by making a "microcapsule" to insulate the sample surface. The method is applied respectively to prepare plan-view TEM specimens of a graphene sheet with multiple adlayers and MoS2 atomic layers. Useful electron diffraction results can be obtained from these specimens for understanding the interlayer orientation relationships in the two materials. Auger electron spectroscopy analysis further confirms that the sample surface is free from contamination under the sufficient protection given by the proposed method.