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My favorite feature of 2012 Navisworks Manage is the Appearance Profiler. It can be used in conjunction with Search Sets to color-code your coordination models. The nice thing is that the settings can be saved out and recalled as needed in the Navisworks NWF file which makes updates to the model much easier. Pre-planning, particularly in file naming conventions, will make this feature update even with the introduction of updated models from the CAD programs. In the figure below, I built search sets based on the file names. Then I assigned those search sets to colors and level of transparency. My architectural model is green and transparent, with electrical in red, ductwork in blue and steel in yellow. Last step, SAVE the profiles listed in the Appearance Profiler to a DAT file that can be imported to any NWF when needed.