A system and method for identifying and manipulating logic analyzer data from multiple clock domains is presented. A logic analyzer receives debug data and determines whether the debug data is a full frequency data type, a half frequency data type, or a crossed data type. Once determined, the logic analyzer reconstructs the debug data such that debug condition-matching logic may process the reconstructed data in a full frequency domain. For half frequency data types, the logic analyzer adds masked data values to the data in order to reconstruct the data into to the full frequency domain before processing the data. For crossed data types, the logic analyzer reconstructs the data into its original format before processing the data in a full frequency domain.