1. A computer implemented method comprising: managing one or more virtual layers in a client computer by a virtualization agent included in the client computer, the virtualization agent being configured to make applications that reside in active virtual layers available and indistinguishable from conventionally installed applications by redirecting system calls for the application's files, processes, and settings to a predetermined redirection area of a corresponding virtual layer; initiating a backup procedure on a backup server to backup selected data corresponding to a selected virtual layer of the one or more virtual layers on the client computer; sending backup messages corresponding to the selected data to the client computer, responsive to the procedure; receiving the backup messages at a backup agent on the client computer from the backup server; in response to the backup agent on the client computer determining the selected data corresponds to the selected virtual layer of the one or more virtual layers, the backup agent: communicating with the virtualization agent in order to identify one or more files that correspond to the selected virtual layer; retrieving the one or more files; and sending the one or more files to the backup server.