*boundaryLayout* is a highly requested Cytoscape 3.X application which boasts a custom boundary-constrained force-directed layout. Boundaries, represented as Cytoscape annotations, may be automatically generated or defined by the user, who can later save and modify them as a “template”, or a collection of boundaries. Whether it be a dynamic subcellular localization template, an n-partite graph to group nodes, or any other configuration of boundaries, *boundaryLayout* supports any user-defined compartmentalization. The force-directed algorithm is derived from the prefuse algorithm, which is used in other applications such as setsApp. Additionally, the user is able to tune numerous algorithmic parameters in the layout settings menu: an effective way to emphasize certain inputs of the layout algorithm including the strengths of different forces such as node-node springs and boundary walls, the number of force iterations, node mass, or the network’s outer bounds thickness. The user can further save, export, and manage their templates through the Boundaries menu; a default Cell Template is provided to the user. For instructions on how to use *boundaryLayout*, visit the [http://www.rbvi.ucsf.edu/cytoscape/boundaryLayout/index.shtml RBVI] (Resource for Biocomputing, Visualization and Informatics) website.