Molecular ruler nanolithography is a unique process capable of extending the achievable resolution of conventional lithography techniques. This is accomplished by patterning functional host structures whose dimensions can be tailored by systematically assembling engineered organic molecules of precise length on their surface, creating a template for producing features with reduced dimensions. We introduce a novel method for implementing molecular ruler lithography using a new sacrificial multilayer host structure. In particular, we demonstrate, using contact lithography, that host structures incorporating an underlying sacrificial resist can be used in conjunction with chemical solution phase self-assembly of a multilayer molecular ruler film, consisting of alternating layers of mercaptodecanoic acid molecules linked with copper ions. This new approach provides several advantages, including the potential for high yield processing, simplified removal of the parent host material, isolation of the host material from the substrate surface, and the capability to pattern daughter features whose thickness exceeds the thickness of the assembled molecular film. This new process can be implemented to create a wide variety of nanoscale structures and devices.