A number of current technological challenges require the development of materials with well-defined nanoscale structure. For example, separation processes rely on materials with well-defined pore sizes and/or interactions, and poor structural control results in limited selectivity between ions and molecules of similar charge and/or size. Photochemical and electrochemical remediation processes rely on specific interactions with molecular targets, but current materials provide poor molecular specificity. Here, I report on the chemistry, processing, and physical processing of an emerging class of organic material that can address these challenges and limitations. Covalent organic frameworks (COFs) are crystalline, organic materials with a well-defined molecular level structure and porosity, and they provide a potential solution to limitations in structure and specificity in polymers and other organic materials. However, they present unique challenges in terms of synthesis and processing. I present recent advances in the synthesis, processing, and stability of COFs. I will demonstrate how COFs can be processed to produce porous and crystalline thin films, and also demonstrate recent findings related to the fragility and stability of COFs under different environmental conditions. Finally, I discuss the application of COFs for separations and photochemical degradation of molecular targets. This work highlights the significant potential of COFs for a variety of applications that rely on molecular recognition and specificity.