The effective use of Run Time Reconfiguration (RTR) in modern FPGAs opens up new avenues to design area and power efficient high performance architectures. However the current design flow for exploiting RTR in designs, leads to the problem of silicon Defragmentation. We propose a silicon compaction/defragmentation technique which works on already placed and routed modules to generate partial bitstreams (programming files) for the device. We have outlined a method which generates these partial bitstreams very fast taking into account the size and position of the "free" silicon when the device is in operation. The other advantage of this method is that the changes in the basic FPGA fabric needed to implement this defragmentation strategy are (almost) trivial.