A semiconductor device has a substrate and a first semiconductor layer with a high resistivity, such as an epitaxial layer with a resistivity in the range of 3000-5000 ohms/cm2, formed over the substrate. A second semiconductor layer is formed at least partially in the first semiconductor layer. A capacitor is formed at least partially over the first semiconductor layer. The capacitor has a plurality of trenches extending through the first semiconductor layer and into the substrate, and a first insulating layer formed in the trench. The trenches can be parallel, serpentine, or other geometric shape. The capacitor also has a second insulating layer formed over the first insulating layer, and a polysilicon layer formed over the second insulating layer. A conductive layer is formed over the capacitor. The first semiconductor layer with high resistivity provides a vertical path to discharge high voltage events incident on the capacitor.