There is a post at 12robots.com for how to add resource navigator filters to CFBuilder:
The solution below is similar, but does not involve accessing .jar files.
Step 1: Locate your version of CFBuilder by selecting “About Adobe ColdFusion Builder 2”. Make a note of the Version and Build numbers. For this post I am on Version: 2.0.0 and Build: 277745
Step 2: Locate the plugin.xml file in the com.adobe.ide.coldfusion.rcp_X.X.X.XXXXXX folder (Notice how X.X.X.XXXXXX corresponds to the Version and Build from Step 1):
com.adobe.ide.coldfusion.rcp_2.0.0.277745
Step 2: Locate the following section:
<extension
point="org.eclipse.ui.ide.resourceFilters">
Step 3: Add a block like this for each new filter you want:
<filter
pattern="_notes"
selected="true"/>
Step 4: Start CFBuilder from the command line. For me on the Mac I execute the following command in Terminal:
"/Applications/Adobe ColdFusion Builder 2/CFBuilder.app/Contents/MacOS/CFBuilder" -clean
Step 5: Enjoy your new navigator filter(s).