Is there a website that I can go to for an application on getting what is called "secret Clearence" Or can I only get that through the company I plan on applying at?

From what I remember, from a former job, is that you work toward that "secret clearance" with the company you go to work for. Obtaining that clearance may take up to a year and as little as three months. Even then information will only be available to you on a "need to know" basis.

And there are many various levels of national secuity clearance levels, secret is merely one ( and not that high if I reemmber right)

You can get a clearance though the government, but normally a company you are going to go to work for will help with your application process.
But as noted, they will take a long time, my first second for a very high rating took amost a year and a half and that was after already having a basically clearance.

The cost for clearance backgrounds can be high. My husband's is Top Secret and took 3 years (but his clearance application started a week before 9/11.)

If there is something you are concerned about disclose it first. They are much more understanding if you tell them there is something no so great there, than if they find it later.

**Edit**

Sorry, just noticed the date on this was kind of old.

Are you referring to a security clearance or what? If you need to be cleared to work on national secrets, the company hiring you will do the background check to have you "vetted".