Methods of forming waveguide connectors include positioning a polymer waveguide in one or more insertion structures within an inner portion of a cap where the polymer waveguide has alignment features on a connection end face corresponding to one or more components of an assembled connector. The method can include inserting a ferrule into the inner portion of the cap such that an inner wall of the cap seals around the assembled connector to prevent contaminants from entering the inner portion and heating the polymer waveguide and the ferrule to a first temperature with the ferrule comprising alignment features and having a different coefficient of thermal expansion from the polymer waveguide. The alignment features of the polymer waveguide align with the alignment features of the ferrule when the polymer waveguide and the ferrule are heated to the first temperature.