Techniques are provided for identifying and removing one or more layers of a software appliance. Layers may be identified and removed quickly and efficiently, without disrupting the distribution or provisioning of the software appliance, and without disrupting desired operations of the software appliance as a whole. In various implementations, it may be necessary or desirable to re-package the same or modified layer(s) within the software appliance at a later point in the distribution cycle of the software appliance. For example, one or more operating system layers may be identified and removed from a software appliance. Then, when the software appliance is distributed and provisioned in a cloud or other network context, a same or different version of the operating system layer(s) may be utilized in re-packaging the software appliance for one or more customers.