Microdosimetry is an extremely useful technique, used for dosimetry in unknown mixed radiation fields typical of space and aviation, as well as in hadron therapy. A new silicon microdosimeter with 3D sensitive volumes has been proposed to overcome the shortcomings of the conventional Tissue Equivalent Proportional Counter. In this article, the charge collection characteristics of a new 3D mesa microdosimeter were investigated using the ANSTO heavy ion microprobe utilizing 5.5 MeV rm He2 + and 2 MeV rm H + ions. Measurement of the microdosimetric characteristics allowed for the determination of the Relative Biological Effectiveness of the 12rm C heavy ion therapy beam at the Heavy Ion Medical Accelerator in Chiba (HIMAC), Japan. Well-defined sensitive volumes of the 3D mesa microdosimeter have been observed and the microdosimetric RBE obtained showed good agreement with the TEPC. The new 3D mesa 'bridge' microdosimeter is a step forward towards a microdosimeter with fully free-standing 3D sensitive volumes.