A method of pruning nets in a circuit design includes, in part, receiving data representative of net layers associated with the circuit design, and accessing a connect database associated with the circuit design. The connect database includes data representative of electrical connections associated with the circuit design. The method further includes, in part, determining whether a marker layer exists in the net layers, and pruning nets that are not connected to the marker layer if the marker layer is determined to exist. The marker layer, which is not stored in the connect database, designates a connection between at least a pair of nets in the circuit design.