Actually, Top Secret is not very high (e.g. well below DOE Q or of course TS/SCI).
Basically, you just have to be honest in your application, and of course you have to be a reasonably trustworthy person (and not black-mailable; e.g. it's OK to be GLBT, but not in the closet).
As noted elsewhere in the comments, you'll have to fill out a long form, people you know will be interviewed (my knowledge of all this is mostly from supplying interviews for a couple of friends), and as noted it will take some time. You won't be able to work on your actual project until you get the clearance, which many find annoying, but for this sort of job perhaps they'll have you learn the development environment, work on tools, etc. (I had one friend give up on a LLNL sysadmin job because he couldn't do anything to speak of.)
If you're concerned about accepting a job that you might end up being let go from because you didn't get your clearance, check out this page: http://www.home.earthlink.net/~lastone2/individualsales.html and the general web site of LeRoy A. Stone: http://home.earthlink.net/~lastone2/home.html.
He provides a service that will give you an estimate of how likely it is you'll get a clearance. I used him back in 2003, although his assessment became moot when my job offer essentially went poof.
One really important aspect of this job: it's a two-fer in terms of having a long career in software. The embedded community has more respect for gray hairs than any other, and work that requires a clearance by definition can't be outsourced overseas or given to H-1B or L-1 visa holders.