A backup manager backups file systems of virtual machines running on a base computer. In order to backup a virtual machine, the backup manager identifies the file on the base machine that represents the virtual machine, freezes the virtual machine, and creates a snapshot thereof. The backup manager restarts the frozen machine, and starts the snapshot. The files of the file system of the snapshot are mapped at a virtual machine level, and the resulting file mapping information is used to backup the files of the virtual machine at a base machine level. The mapping information is current as of the instant the snapshot was taken. The backup manager can backup one, multiple or all virtual machine(s) running on the base computer, in conjunction with a full or incremental backup of the base computer, or independently.