An automated system is presented for unit testing an application in a mainframe execution environment. The system includes a test configurator, a stub setup routine and an interceptor routine. The test configurator is configured to receive and parse a test input file, where the test input file includes a record for a particular file accessed by the application using the given type of file system. Upon reading the record, the test configurator calls the stub setup routine. The stub setup routine is associated with the given type of file system and creates an object for the particular file in the mainframe execution environment, such that the object is instantiated from a class representing the given type of file system. The interceptor routine is accessible by the application. In response to a given command issued by the application for the given type of file system, the interceptor routine operates to interact with methods provided by the object.