Quantify Tool - Controlling Levels

Hi, I am writing from MTA in New York City and this is my first post. My question is regarding the Quantify tool. How do I turn off the levels in reference files which I do not want to have included in my report? I was told that if I turned off the levels I didn't want to quantify in any particular view, hit 'Set From' in the tool settings and set the tool settings to that particular view, then only the levels in that view would be calculated. However, when I tried it that wasn't the case. Only levels that are active levels in the master file are able to be controlled. There are no levels from reference files displayed in the "Quantified Levels" area of the dialogue, so therefor they cannot be turned off. How do we control levels in reference files when we are performing Quantification? Thanks, Marc