Perfluorocyclobutyl (PFCB) polymers and copolymers enjoy a unique combination of properties well suited for optical applications such as high temperature stability, precisely controlled refractive index, low moisture absorption, excellent melt and solution processability, a variable thermoptic coefficient, and low transmission loss at 1300 and 1550 nm. Copolymerization reactions offer tailored thermal and optical properties by simple choice of comonomer. PFCB copolymers can be solution or melt microfabricated via standard methods and can also be processed via micro-transfer molding in photolithographically generated features. Reliable molding of polymer waveguides offers significant potential to reduce photonic integrated circuit (PIC) fabrication costs and enable the realization of compact, integrated subsystems for a variety of applications. Copolymerization chemistry, thermoptic measurements, and initial results on the first micro-transfer molded waveguide structures are presented.