The present invention provides novel etching techniques for etching SinullGe, employing SF6/fluorocarbon etch chemistries at a low bias power. These plasma conditions are highly selective to organic photoresist. The techniques of the present invention are suitable for fabricating optically smooth SinullGe surfaces. A cavity was etched in a layer of a first SinullGe composition using SF6/C4F8 etch chemistry at low bias power. The cavity was then filled with a second SinullGe composition having a higher refractive index than the first SinullGe composition. A waveguide was subsequently fabricated by depositing a cladding layer on the second SinullGe composition that was formed in the cavity. In a further embodiment a cluster tool is employed for executing processing steps of the present invention inside the vacuum environment of the cluster tool. In an additional embodiment a manufacturing system is provided for fabricating waveguides of the present invention. The manufacturing system includes a controller that is adapted for interacting with a plurality of fabricating stations.