A logically hierarchical netlist may be split along physical partition boundaries while retaining information on the logical hierarchy. Nets can be driven to higher levels of hierarchy in order to maintain connectivity and enable the original logical function. A mapping of nets can be created. During the design process merging of physical partitions may result in a new logically hierarchical netlist which retains the hierarchy of the original logically hierarchical netlist. The lowest common hierarchical ancestor (LCA) is identified and then the appropriate cells and nets are included during the merging process.