The purpose of the CIA polygraph is to extract derogatory information from you that the adjudicators could not have known simply based upon a SSBI (Sf-86) background check. The polygraph is not able to detect lies and the polygraphers know it. The polygraphers merely exploit the ignorance and gullibility of people into believing that it really is a lie detector. 

When the applicant's physiological response rises on a particular question, the polygrapher will use that as an opportunity to accuse the applicant of being a liar. The polygrapher will press the severity of the applicant's situation by stating s/he only has two options: either s/he can leave the room and lose the clearance or s/he can stay and confess to the polygrapher what s/he was withholding. The applicant will obviously choose the second option, but this only paves the way for the polygrapher to interrogate the applicant and extract all different kinds of personally shameful and embarrassing behavior. 

The polygrapher will say all kinds of rhetoric to warp the applicant's sense of reality. The polygrapher might say, "You are going to tell us things that you have never told anyone in your entire life. You have to tell us the deepest and darkest things you have ever done in order to eliminate any stimuli when you take your second polygraph. We are only trying to help you." This is a complete lie. They are actually attempting to find derogatory conduct that they will use against you. 

Just keep in mind to never tell them anything that you think could cause your clearance to be denied. To not fall for their honest sounding jargon used to get you to share your most shameful conduct. Every derogatory thing you tell them will be part of your official investigative file, which will be shared with other agencies through the Scattered Castles database. 

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Don't hold your breath. In any case, I would wager substantially that any appeal to the CIA will be unsuccessful.   Since the CIA is a law unto itself, you might well have a chance at getting a security clearance at another federal agency.