Patent ID: 7349614

Claim:
A method to form a waveguide with an embedded mirror in the manufacture of an optical substrate device, said method comprising: forming a cladding layer overlying a silicon layer on an optical substrate; patterning said cladding layer to form openings through said cladding layer where an embedded mirror is planned; depositing a waveguide layer overlying said cladding layer and filling said openings; patterning said waveguide layer to define a waveguide wherein said patterning forms an angled edge where said waveguide layer is etched through to underlying said cladding layer; depositing a metal layer overlying said waveguide; patterning said metal layer to remove said metal layer from said waveguide excepting at said angled edge of said waveguide wherein said metal layer forms an embedded mirror for said waveguide; and depositing a second cladding layer overlying said waveguide wherein said waveguide has parallel trenches or is based on a photonic crystal device and wherein chemical or biological agents are trapped in said trenches or in holes in said waveguide or photonic crystal device to thereby affect evanescent light when an optical signal is transmitted in said waveguide.