In this work we present a technique for optically modulating a terahertz pulse inside a parallel plate waveguide. A novel semiconductor filled waveguide is formed by coating both sides of a thin, high resistivity silicon slab with a transparent conducting oxide. While the waveguide is intrinsically lossy due to the low conductivity of the oxides, it permits photoexcitation through the plates, generating free carriers within the silicon that modulates the terahertz pulse transmission. We demonstrate this modulation by observing the Drude response of photoexcited carriers within the silicon in a narrow strip inside the waveguide.