For the first time, new epitaxial graphene nanostructures resembling charged “bubbles” and “domes” are reported. A strong influence of the change in morphology on the graphene layer’s electronic, mechanical and optical properties has been shown. The morphological properties of these structures have been studied with Atomic Force Microscopy (AFM), Ultrasonic Force Microscopy (UFM) and Raman spectroscopy. After initial optical microscopy observation of the graphene surface distortions , a detailed description of the surface morphology, via AFM and nanomechanical UFM measurements, was obatined, allowing identification of new graphene nanostructures - domes and bubbles ranging from few tens of nanometres (150 - 200 nm) to few µm in size. The AFM topographical and UFM stiffness data implied the freestanding nature of the graphene layer within the domes and bubbles, with a height on the order of 5 - 10 nm. Raman spectroscopy mappings of G and 2D bands and their ratio confirm not only the graphene composition of these structures but also the existence of step bunching, defect variations and the carrier density distribution. In particular, it indicates that inside the bubbles and substrate there arises complex charge redistribution, in fact, the graphene bubble-substrate interface forms a charged capacitance. We have determined the strength of electric field inside the bubble - substrate interface which may lead to a mini-gap opening of the order of 5 meV for epitaxial graphene grown on 4H-SiC face terminated carbon.