Here we present the Scientific Filesystem (SCIF), an organizational format that supports exposure of executables and metadata for discoverability of scientific applications. The format includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. SCIF makes it easy to expose metadata, multiple environments, installation steps, files, and entrypoints to render scientific applications consistent, modular, and discoverable. A SCIF can be installed on a traditional host or in a container technology such as Docker or Singularity. We will start by reviewing the background and rationale for the Scientific Filesystem, followed by an overview of the specification, and the different levels of internal modules (“apps”) that the organizational format affords. Finally, we demonstrate that SCIF is useful by implementing and discussing several use cases that improve user interaction and understanding of scientific applications. SCIF is released along with a client and integration in the Singularity 2.4 software to quickly install and interact with Scientific Filesystems. When used inside of a reproducible container, a Scientific Filesystem is a recipe for reproducibility and introspection of the functions and users that it serves.