We report on the first through-wafer silicon-based Electrostatic Quadrupole Array (ESQA) to focus high energy ion beams. This device is a key enabler for a wafer based accelerator architecture that lends itself to orders-of-magnitude reduction in cost, volume and weight of charged particle accelerators. ESQs are a key building block in developing compact Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) [1]. In a MEQALAC electrostatic forces are used to focus ions, and electrostatic field scaling permits high beam current densities by decreasing the beam aperture size for a given peak electric field set by breakdown limitations. Using multiple parallel beams, each totaling to an area A, can result in higher total beam current compared to a single aperture beam of the same area. Smaller dimensions also allow for higher focusing electric field gradients and therefore higher average beam current density. Here we demonstrate that Deep Reactive Ion Etching (DRIE) micromachined pillar electrodes, electrically isolated by silicon-nitride thin films enable higher performance ESQA with waferscale scalability. The fabricated ESQA are able to hold up to1 kV in air. A 3*3 array of 12 keV argon ion beams are focused in a wafer accelerator unit cell to pave the way for multiple wafer accelerator.