1. A method for associating a file type of a file with one or more programs, the method comprising the steps of: (a) intercepting a request from a process executing on a computing device configured with an isolation environment, the isolation environment comprising a user isolation layer and an application isolation layer, to store in a native configuration store residing on a memory element provided by the computing device file type association information associated with a system scope; (b) determining from the request an application program associated with one of either of a user isolation scope, an application isolation scope and the system scope to be associated with a file type in the native configuration store; (c) writing to the native configuration store, specific to one of either of the user isolation scope, the application isolation scope and the system scope, an association of the file type with a chooser tool; (d) selecting, by a process executing on behalf of a user and in the context of the application isolation scope and the user isolation scope, a file including a file type to invoke the application program, and invoking the chooser tool in response to selecting the file; and (e) displaying by the chooser tool a list of one or more application programs associated with the file type, wherein the chooser tool executes in the context of one of either of the application isolation scope and the user isolation scope, and the list is specific to one of either of the user isolation scope and one or more application isolation scopes.