Endpoint virtualization aware backup

A system and method for efficiently utilizing endpoint virtualization information during backup operations. A computer system includes a backup server that permits the identification, browsing and selecting of files within virtual layers. Examples of virtual layers comprise at least a user data layer, an applications layer, and an operating system layer. Backup messages are sent to a corresponding client computer to backup the selected files or layers. The client computer includes a virtualization agent configured to manage one or more virtual layers in the client. In response to determining the selected data corresponds to a virtual layer of the one or more virtual layers, a backup agent in the client is configured to communicate with the virtualization agent in order to identify one or more files that correspond to the virtual layer, retrieve the one or more files, and send the one or more files to the backup server. The backup server is further able to create a different backup schedule for each virtual layer. Also, during an incremental backup of data in a virtual layer, the client computer is configured to ignore files outside of the virtual layer.