Do you mean on the fly? Or destructively apply it?
Either should work:
To do it on the fly, you may need to use a bus and adjust the volumes accordingly. Using envelopes you should be able to send the portion of the file to be affected to a bus with the plug on it. And not send it the other portion of the time.
Or Desructively, select the area in question and process it, or apply the effect as it were. It should only apply to the highlighted materail.
All else fails, cut the file, and put the area in question on another track, perfectly aligned of course, and have that track have the plug-in on it. You should not be able to tell the difference.
You got options.