Thin ion transmission detectors can be used as a part of a telescope detector for mass and energy identification but also as a pre-cell detector in a microbeam system for studies of biological effects from single ion hits on individual living cells. We investigated a structure of graphene on silicon carbide (SiC) with the purpose to explore a thin transmission detector with a very low noise level and having mechanical strength to act as a vacuum window. In order to reach very deep cavities in the SiC wafers for the preparation of the membrane in the detector, we have studied the Inductive Coupled Plasma technique to etch deep circular cavities in 325 μm prototype samples. By a special high temperature process the outermost layers of the etched SiC wafers were converted into a highly conductive graphitic layer. The produced cavities were characterized by electron microscopy, optical microscopy and proton energy loss measurements. The average membrane thickness was found to be less than 40 μm, however, with a slightly curved profile. Small spots representing much thinner membrane were also observed and might have an origin in crystal defects or impurities. Proton energy loss measurement (also called Scanning Transmission Ion Microscopy, STIM) is a well suited technique for this thickness range. This work presents the first steps of fabricating a membrane structure of SiC and graphene which may be an attractive approach as a detector due to the combined properties of SiC and graphene in a monolithic materials structure.