1. A method for creating thin clones of a virtual machine (VM) using the VM's associated storage system to copy and deduplicate storage for the thinly cloned VMs, comprising: creating a base VM in a directory of a storage container attached to a hypervisor; mapping the storage container to a volume on a storage system; copying files associated to the base VM into one or more desired locations within the storage container using a snapshot of the respective files associated to the base VM, comprising: creating metadata that identifies physical storage locations of the files associated to the base VM; and copying the metadata to the one or more desired locations within the storage container; customizing the one or more cloned VMs by modifying the respective one or more VMs' parameters; and registering the one or more cloned VMs within the hypervisor.