Embodiments of the invention include a method of using a sensor. The method includes accessing a sample and exposing the sample to the sensor. The sensor includes a sensing circuit having with a field effect transistor (FET) having a gate structure. A cavity is formed in a fill material that is over the gate structure. A probe of the sensor is within a portion of the cavity. An upper region of the probe is above a top surface of the fill material, and a lower region of the probe is below the top surface of the fill material. The probe structure includes a 3D sensing surface structure, and a liner is formed on the 3D sensing surface and configured to function as a recognition element. A portion of the liner is on the lower region of the probe and positioned between sidewalls of the cavity and the 3D sensing surface.