I'll give you information about the process for obtaining a clearance.
SECRET:
NAC - National Agency Check - they'll take your fingerprints and name and run them through national crime databases (FBI database, NICS, etc) to check for any warrants.
LAC - Local Agency Check - they'll contact the police departments of any place in which you've lived, worked, or gone to school, and ask for a report of all contact they've ever had with you.
Credit check - they'll run your credit report to make sure you can't be easily bought out (ie, a hostile state offers to pay off your credit card in exchange for just a tiny bit of information).
TOP SECRET
The above, plus:
Field investigation - they'll contact the references you list and your neighbors for the past 7 years, and ask them a series of questions about you and your habits. They'll ask for recommendations to other people who have known you. They are trying to obtain a negative and positive view of your personality and habits to present to the Adjudicator.
Subject interview - speaks for itself.
Education - independent verification of all educational background claims.
Employment - independent verification of all past employment, including personal interviews of 2 colleagues where possible, and where employment exceeded 6 months.
For both, the Adjudicator will determine whether you are suitable for access to confidential information based on the guidelines listed here: http://fas.org/sgp/spb/class.htm If, based off those guidelines and the information they will collect, you feel that you will get rejected, then yes, you are wasting your time. If not, though, or if it's a "gray area," there should be a liaison you can talk to.
For Secret clearances, expect a wait time of 1-3 months (depending on how many previous addresses you have), and for TS clearances, expect to be waiting 6 months to 18 months (depending on the number of previous residences AND on whether something nasty pops up - ie, a past illicit drug use).
Source(s):
AD NCO serving in the USAF; I have a TS clearance
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