A fault tolerant system is described for deploying an application contained in an application storage volume, which may be a virtual disk, on a virtual machine (VM) in a remote desktop environment. The application can be executed on the VM after mounting the virtual disk. A backup of the virtual disk is produced by cloning the virtual disk to a different storage device than the location of the primary virtual disk. In some embodiments, if the primary virtual disk fails during execution of the application, the application is suspended, redirected to the backup virtual disk, and resumed from the backup virtual disk. In other embodiments, if the primary virtual disk fails during execution of the application, a child process is spun off from the parent process using forking techniques, the child process is directed to the backup virtual disk, and the application is resumed from the backup virtual disk.