A method enables a central management service to operate on individual files within virtual disks associated with different virtual machines (VMs) running in one or more host computers that are each networked to a remote storage system. An IO request from a VM is received at a virtualization software layer on a host computer, wherein the IO request relates to a file stored in a virtual disk associated with the VM, and the file is individually stored in the remote storage system in accordance with a file system. The central management service is notified of the received IO request and uses the file system to access the file in the remote storage system to perform a management task on the file, and the IO request is then performed on the file by the virtualization software layer upon a notification of a successful completion of the management task.