Integration of low dielectric constant Benzocyclobutene (BCB) film with deep etched structures in silicon allows the fabrication of MEMS devices with low parasitic loss. A fabrication process is developed for integration of thin BCB film and deep anisotropically-etched grooves in silicon using potassium hydroxide (KOH). Gold (Au) is used as an etch mask to protect the low-k film during the highly-corrosive, long, and high-temperature KOH etching process. Metal/BCB adhesion is a key parameter in this masking design. Adhesion of the BCB and metal mask was improved by cure management of the BCB before and after metallization, surface treatment of the BCB before metallization, and high-temperature metallization. Test structures were fabricated to demonstrate the feasibility of this fabrication process. Adhesion improvement was successfully verified by studying BCB/metal interface using time-of-flight secondary ion mass spectroscopy and Auger electron spectroscopy. This study enables the development of the next generation micromotors/microgenerators.