Freefilter only works properly if you do things exactly this way..
Figure out what mix posesses the quality you are going for, really the only thing it will do is mold your final EQ to be more like the source mix, so keep that in mind. It can make a big difference but it can also do unpredictable or undesirable things to your mix so you may have to do a bit of molding afterwards.. and that is why the equalizer is there..
Now that you have the song you want to use as your source, import it as a stereo track in Nuendo. do it as a new session or temporary addition to your mix, muting the other tracks. Apply FreeFilter as an effect, to the master or to the track channel, doesn't matter..
Before you do anything else, get the following rule stuck in your head. As soon as you have made a profile of either the source or destination mix, you should always disable the plugin for a moment. Otherwise, you will see it lose the profile you have just made, because it is trying to read the silence.
SO, keeping that in mind, click the "Log" button for logarhythmic mode (it is more useful, imo) then click "Source", make sure the plugin is enabled, then hit play. Once you've played a good portion of the song, and the waveform stops doing much changing, disable the plugin and hit stop. The profile is now preserved.
Make a preset so that this setting will be available to you for all future mixes.
Ditch the source mix and load your own mix up again. Load Freefilter on the master. Disable the plugin if it isn't. Call up the preset. Hit the "Destination" button. Enable plugin. Hit play. Disable when it's got the profile. Switch to "Match". Now you can play with the dial up top that says "Morph %". You don't want to go overboard. Start off at 0%, enable the plugin, hit play. Your mix should sound as it did. Bring the dial up slowly. Between 40% and 80% should be ideal. Trust your mixing abilities, if you can't, this plugin is useless to you. It should be a molding tool, not surgery. Listen to see if there's any ugly frequencies sticking out, if so, fix them with the equalizer. Roll off below 50hz, and tame your high end if necessary. Gloss is good, sibilance and nasalness are not. Minimize the plugin, add whatever compression you're gonna do in the chain AFTER Freefilter preferably..
Good luck.
