According to a system and method, for composing a virtual disk for a virtual desktop, the virtual desktop is booted from a virtual disk comprised of a base disk image and a user delta disk image that receives all disk writes to the virtual disk. Disk space is allocated on the virtual disk for a file associated with a selected application to be provided to a user of the virtual desktop. Then the virtual desktop is recomposed offline by linking the bass disk image, an application delta disk image including the file associated with the selected application, and the user delta disk image. The recomposing includes modifying meta data of the application delta disk and the user delta disk so that the file associated with the selected application is mapped to the disk space previously allocated.