This article describes methods to process a THz hologram of low absorbing objects recorded with an optically pumped laser with four emission lines in the 1.39-4.25 THz range and a nanometric FET detector in 65 nm CMOS with an integrated patch antenna. Two and four-step phase shifting methods are applied to reconstruct the multifrequency holograms into one false-colored image that reveals information about the objects. The images are further refined by removing noise information including the DC term and the conjugate beam information. These methods are demonstrated by inspecting stacked low absorbing graphene layers on a high resistivity silicon substrate.