We investigate highly confined and isolated surface modes in a phononic crystal plate based on pillars with cap layers. The structure is made of a thin membrane supporting periodic pillars each composed of one cylinder surmounted by a disk shaped cap layer. An optimal choice of the geometrical parameters and material composition allows the structure to support isolated radial contour modes confined in the cap layer. In this study, we consider diamond and gold (Au) as the pillar and cap layers, respectively, and aluminum nitride as a thin membrane owing to the strong contrast in their elastic and density properties and to their compatibility with the integrated circuit technology and microwave electroacoustic devices. The phononic crystal based on diamond pillars allows us to induce a wide stop band frequency, and the addition of the Au disk shaped layer on diamond pillars enables us to introduce flat modes within the bandgap. We demonstrate that one can optimize the flat mode frequencies by varying the geometrical parameters of the Au cap layer. The quality factor (Q) of a cavity resonator composed of one line gold/diamond pillar surrounded by an array of diamond pillars on both sides has been investigated. These results clearly show that, using this design approach, one can (i) reduce the acoustic energy leakage out of the resonator and (ii) optimize the cavity resonator’s Q factor by varying only the geometrical parameters of the gold cap layer. The proposed design provides a promising solution for advanced signal processing and sensing applications