A method and system for updating a virtual machine that is utilized as a base virtual machine for one or more linked clone virtual machines. The method comprises deploying the base virtual machine on a host system, the base virtual machine comprising a base virtual disk which is attachable to the one or more linked clones and a base delta disk. The method further comprises deploying a software update to the base delta disk of the base virtual machine and once the software update is deployed to the base delta disk of the base virtual machine, shutting down the base virtual machine. The method further comprises updating the base virtual machine by merging the software update deployed on the base delta disk of the base virtual machine with the base virtual disk of the base virtual machine.