Hernan. I didn't reply earlier as I'm no expert on this subject. I can remove a complete airport but that's as far as I go. The guys on the FSSC support forum know far more than me.
As you know, you can do this by manually adding an Exclude switch to Scenery.cfg.
what follows, is it: all, or items, or objects?
objects would remove scenery objects like default buildings. With this method it's sometimes difficult to be accurate enough to remove individual buildings. In FSSC I think it would be easier to use the Exclusion feature. Right-click/New Misc Object/Exclusion brings up this options window.

Check the Visual Scenery option to remove buildings. You can resize the Exclusion area & position it as necessary.
PS. Think I misunderstood your question. Most 3rd party scenery includes instructions for adding the Exclude switch if necessary. It's usually a matter of copy/pasting the full Exclude= entry from the Readme file into Scenery.cfg.