Well, we all have done stupid things in our past, I just have never been convicted of anything

If you have no criminal record, why would you have an FBI file? (If you ever applied for FBI employment you would have an FBI HQ file, but you didn't mention this.) In any event, when you apply for a security clearance, a National Agency Check will be conducted, and if you have an FBI file, your background investigators will learn about it and no doubt request it.

I should add that I have NO criminal record. In fact, I would love to obtain my FBI file to wave in these peoples faces if you happen to know where I could obtain it. I have skimmed/downloaded the book and the article you wrote/referred me to and just want ot say thanks for the reply and site, nice to know I'm not alone

I can't really offer any advice on whether you should agree to any polygraph examination, but you should at least make an informed decision. You'll find the polygraph process described in detail in The Lie Behind the Lie Detector. See also my article "The Lying Game: National Security and the Test for Espionage and Sabotage" which discusses the specific polygraph technique used by DOE for counterintelligence screening.

Am applying for DOE clearance. I've been denied once already, due to substance abuse. Told truth about every drug I've ever tried(fairly extensive list) and have quit all but cigarettes,beer, and coffee. Deemed susceptible to blackmail and therefore a security risk due to diagnosis of alcoholism by DOE psychaitrist. My boss of 4 YEARS says he cannot justify firing me for lack of security clearance, yet wants me to re-apply. DOE will want proof of alcohol treatment/habits and I suspect a polygraph. Should I refuse, or try to pass?