The invention relates to a method and a system of handling a silicon-based wafer and a method of packaging semiconductor. A silicon-based wafer has a first and second surfaces wherein a glass carrier is mounted on the second surface by a UV tape. The method of handling a silicon-based wafer comprises holding the silicon-based wafer by a vacuum holder applied on the first surface of the silicon-based wafer; removing said glass carrier from the silicon-based wafer by irradiating said UV tape with a UV beam through the glass carrier, thereby releasing the UV tape; flipping the silicon-based wafer; placing the silicon-based wafer onto a vacuum plate; securing the silicon-based wafer on the vacuum plate by applying vacuum to the vacuum plate; and releasing the vacuum holder from the silicon-based wafer. The invention further provides a method of packaging a semiconductor and a system of handling a silicon-based wafer. A rigidity demanded by the silicon-based wafer from which the glass carrier is removed is provided by vacuum substrate, thereby reducing breakage of the medium layer in the through-silicon medium window.