The use of integrated waveguides with a limited interaction region in contact with a sensitive medium presents great potentialities for the development of optical sensors. In this paper, we describe a new fabrication process of ion-exchange waveguides well suited for integrated sensor applications. The principle of fabrication is as follows. During the first step, a channel waveguide is generated at the surface of a glass substrate by thermal ion-exchange. Then a rectangular pattern mask is transferred onto the central portion of the waveguide by standard photolithographic techniques. During the second step, the wafer is immersed in a molten salt and an external electric field is applied across the glass substrate. As the aluminium mask acts as a blocking barrier, only the unmasked regions of the waveguide are buried whereas its central region remains located close to the surface. For a single-mode waveguide at 780nm, we measured propagation losses of 0.13 dB/cm for the buried portion, 2.80 dB/cm for the surface portion and losses of 0.40 dB for the transition region. For this structure, we also observed a deformation of the fundamental mode. The proposed method is easy to implement and permits the topography of the elaborated waveguides to be controlled precisely.